In [1]:
import sys
import os
from itertools import chain
from collections import defaultdict
import numpy as np
import pandas as pd
%matplotlib inline
import matplotlib.pyplot as plt
import seaborn as sns
pd.set_option('precision', 3)
pd.set_option('display.max_colwidth', -1)
import gseapy as gp
import goatools

obodag = goatools.obo_parser.GODag('go-basic.obo')


load obo file go-basic.obo
go-basic.obo: fmt(1.2) rel(2017-03-16) 48,478 GO Terms

In [2]:
sys.path.insert(0, "/home/gstupp/projects/metaproteomics")
from metaproteomics import utils
#from metaproteomics.analysis import build_loci

BASE = '../out/'
grouped_loci = utils.load(os.path.join(BASE,"grouped_loci_filt_norm.pkl.gz"))

In [3]:
def make_go2Gene_map(grouped_loci, ontology='MF'):    

    ontology_map = {'MF': 'molecular_function', 'BP': 'biological_process', 'CC': 'cellular_component'}
    
    out = defaultdict(set)    
    for l in grouped_loci:
        if 'go' in l.annotations:
            for go in l.annotations['go']:
                if obodag[go].namespace == ontology_map[ontology]:
                    out[go].add(l.cluster_id)
                    for parent in obodag[go].get_all_parents():
                        if obodag[parent].namespace == ontology_map[ontology]:
                            out[parent].add(l.cluster_id)
                
    return dict(out)

def filter_go2gene_map(go_locus):
    
    # Remove "very broad" gene sets. Arbitrary definition: gene sets that emcompass >50% of all IDs
    all_ids = set(chain(*go_locus.values()))
    go_locus = {key: value for (key, value) in go_locus.items() if len(value) / len(all_ids) <= 0.5}

    # Remove terms with less than 5 members: changed from 10 to 5 becasue small #s of proteins compared
    # to what you would find wiht genes
    go_locus = {key: value for (key, value) in go_locus.items() if len(value) >= 5}

    # Remove child terms with identical gene sets as their parents
    to_remove = set()
    for parent in go_locus.keys():
        # If child term has exact same members as parent, remove
        child_ids = [x.id for x in obodag[parent].children if x.id in go_locus.keys()]
        for child in child_ids:
            if go_locus[child] == go_locus[parent]:
                to_remove.add(child)
    go_locus = {key: value for (key, value) in go_locus.items() if key not in to_remove}

    # Remove sibling terms with identical gene sets
    to_remove = set()
    to_keep = set()
    for brother in go_locus.keys():
        to_keep.add(brother) # make sure filtered out siblings don't filter out ones we want to keep
        for parent in obodag[brother].parents:
            siblings = set([y.id for y in parent.children])
            siblings.remove(brother)
            for sibling in siblings:
                if sibling in go_locus.keys() and go_locus[brother] == go_locus[sibling] and not sibling in to_keep:
                    to_remove.add(sibling)
    go_locus = {key: value for (key, value) in go_locus.items() if key not in to_remove}

    return go_locus

def gomap_to_csv(go2gene, out_file = 'test.tsv'):

    out = ""
    for term, loci in go2gene.items():
        out += "{}\t".format(term)
        out += "{}\t".format(obodag[term].name)
        out += '\t'.join(list(map(str,loci)))
        out += '\n'
        
    with open(out_file, 'w') as fout:
        fout.write(out)

In [4]:
def run_go_gsea(rank_df, g2g_map, seed, outdir='tmp'):
    """
    A ranked df and go2gene mapping returns the result dataframe for GSEA against all go-Terms
    
    loci must be grouped such that avg_ratio and p-values are correct for 1 phenotype
    see rt_unenr_grouped_loci above for example
    """
    import gseapy as gp
        
    # save the go 2 gene map, since gseapy doesn't seem to be able to use one already in memory
    gomap_to_csv(g2g_map, 'temp.gmt')
    
    res = gp.prerank(rnk=rank_df, gene_sets='temp.gmt', outdir=outdir, min_size = 5, max_size=500, 
                     permutation_n = 10000, graph_num = 20, seed=seed)
      
    def get_go_name(term):
        return obodag[term].name
    
    res['name'] = res.index.map(get_go_name)
    
    return res.sort_values('nes', ascending=False)

def plot_gsea_result(row, rank):
    return gp.plot.gsea_plot(rank, row['name'], row.hit_index, row.nes, row.pval, row.fdr, row.rank_ES, phenoPos='Tcell', phenoNeg='RAG')

In [5]:
mf_map = make_go2Gene_map(grouped_loci)
mf_map_f = filter_go2gene_map(mf_map)

print('Unfiltered: {}\tFiltered: {}'.format(len(mf_map), len(mf_map_f)))

bp_map = make_go2Gene_map(grouped_loci, 'BP')
bp_map_f = filter_go2gene_map(bp_map)

print('Unfiltered: {}\tFiltered: {}'.format(len(bp_map), len(bp_map_f)))

cc_map = make_go2Gene_map(grouped_loci, 'CC')
cc_map_f = filter_go2gene_map(cc_map)

print('Unfiltered: {}\tFiltered: {}'.format(len(cc_map), len(cc_map_f)))


Unfiltered: 596	Filtered: 241
Unfiltered: 751	Filtered: 271
Unfiltered: 103	Filtered: 44

RT vs Control Human/Mouse


In [6]:
out_dir = "RT_control_hm_gsea"
df = pd.read_csv(os.path.join(BASE,"RT_control_results_named_annot.csv"))
df = df[(df.padj.abs()<=0.2)]
df = df[df.human_mouse]
df['log2FoldChange'] = -1 * df['log2FoldChange']
rank_df = df[['Unnamed: 0', 'log2FoldChange']].rename(columns={'Unnamed: 0': 'gene_name', 'log2FoldChange': 'rank'})
rank_df = rank_df.sort_values('rank').reset_index(drop=True)
mf_res = run_go_gsea(rank_df, mf_map_f, seed=1111, outdir=out_dir)
bp_res = run_go_gsea(rank_df, bp_map_f, seed=1111, outdir=out_dir)
#cc_res = run_go_gsea(rank_df, cc_map_f, seed=1111, outdir=out_dir)
mf_rt = mf_res.query('nes > 0 and pval < 0.05').sort_values('nes', ascending=False)
mf_control = mf_res.query('nes < 0 and pval < 0.05').sort_values('nes', ascending=True)
bp_rt = bp_res.query('nes > 0 and pval < 0.05').sort_values('nes', ascending=False)
bp_control = bp_res.query('nes < 0 and pval < 0.05').sort_values('nes', ascending=True)
#cc_rt = cc_res.query('nes > 0 and pval < 0.05').sort_values('nes', ascending=False)
#cc_control = cc_res.query('nes < 0 and pval < 0.05').sort_values('nes', ascending=True)


2017-04-04 12:35:46,520 Parsing data files for GSEA.............................
/usr/lib/python3/dist-packages/numpy/lib/arraysetops.py:379: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
  mask |= (ar1 == a)
2017-04-04 12:35:46,562 0005 gene_sets used for further statistical testing.....
2017-04-04 12:35:46,562 Start to run GSEA...Might take a while..................
2017-04-04 12:35:47,192 Start to generate gseapy reports, and produce figures...
/usr/lib/python3/dist-packages/matplotlib/figure.py:1744: UserWarning: This figure includes Axes that are not compatible with tight_layout, so its results might be incorrect.
  warnings.warn("This figure includes Axes that are not "
2017-04-04 12:35:48,539 Congratulations...GSEAPY run successfully...............
2017-04-04 12:35:48,557 Parsing data files for GSEA.............................
2017-04-04 12:35:48,603 0010 gene_sets used for further statistical testing.....
2017-04-04 12:35:48,603 Start to run GSEA...Might take a while..................
2017-04-04 12:35:50,004 Start to generate gseapy reports, and produce figures...
2017-04-04 12:35:53,020 Congratulations...GSEAPY run successfully...............

In [7]:
mf_rt


Out[7]:
es nes pval fdr gene_set_size matched_size genes name
Term

In [8]:
mf_control


Out[8]:
es nes pval fdr gene_set_size matched_size genes name
Term

In [9]:
bp_rt


Out[9]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0065007 0.576 1.796 0.007 0.042 86 14 [165648111, 165648112, 61499238, 61499613, 61503068, 165636196, 165642139, 165646068, 165661488, 61457133, 61504270, 165661076, 61499612, 165666724] biological regulation
GO:0050789 0.609 1.733 0.009 0.038 80 10 [165648111, 165648112, 61499238, 61503068, 165636196, 165642139, 165646068, 61457133, 61504270, 165666724] regulation of biological process

In [10]:
bp_control


Out[10]:
es nes pval fdr gene_set_size matched_size genes name
Term

RT vs Control Non-Human/Mouse


In [11]:
out_dir = "RT_control_gsea"
df = pd.read_csv(os.path.join(BASE,"RT_control_results_named_annot.csv"))
df = df[(df.padj.abs()<=0.2)]
df = df[~df.human_mouse]
df['log2FoldChange'] = -1 * df['log2FoldChange']
rank_df = df[['Unnamed: 0', 'log2FoldChange']].rename(columns={'Unnamed: 0': 'gene_name', 'log2FoldChange': 'rank'})
rank_df = rank_df.sort_values('rank').reset_index(drop=True)

In [12]:
mf_res = run_go_gsea(rank_df, mf_map_f, seed=1111, outdir=out_dir)
bp_res = run_go_gsea(rank_df, bp_map_f, seed=1111, outdir=out_dir)
cc_res = run_go_gsea(rank_df, cc_map_f, seed=1111, outdir=out_dir)
mf_rt = mf_res.query('nes > 0 and pval < 0.05').sort_values('nes', ascending=False)
mf_control = mf_res.query('nes < 0 and pval < 0.05').sort_values('nes', ascending=True)
bp_rt = bp_res.query('nes > 0 and pval < 0.05').sort_values('nes', ascending=False)
bp_control = bp_res.query('nes < 0 and pval < 0.05').sort_values('nes', ascending=True)
cc_rt = cc_res.query('nes > 0 and pval < 0.05').sort_values('nes', ascending=False)
cc_control = cc_res.query('nes < 0 and pval < 0.05').sort_values('nes', ascending=True)


2017-04-04 12:35:53,341 Parsing data files for GSEA.............................
/usr/lib/python3/dist-packages/numpy/lib/arraysetops.py:379: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
  mask |= (ar1 == a)
2017-04-04 12:35:53,484 0054 gene_sets used for further statistical testing.....
2017-04-04 12:35:53,485 Start to run GSEA...Might take a while..................
2017-04-04 12:36:35,076 Start to generate gseapy reports, and produce figures...
/usr/lib/python3/dist-packages/matplotlib/figure.py:1744: UserWarning: This figure includes Axes that are not compatible with tight_layout, so its results might be incorrect.
  warnings.warn("This figure includes Axes that are not "
2017-04-04 12:36:41,029 Congratulations...GSEAPY run successfully...............
2017-04-04 12:36:41,047 Parsing data files for GSEA.............................
2017-04-04 12:36:41,205 0063 gene_sets used for further statistical testing.....
2017-04-04 12:36:41,206 Start to run GSEA...Might take a while..................
2017-04-04 12:37:28,651 Start to generate gseapy reports, and produce figures...
2017-04-04 12:37:34,033 Congratulations...GSEAPY run successfully...............
2017-04-04 12:37:34,038 Parsing data files for GSEA.............................
2017-04-04 12:37:34,072 0024 gene_sets used for further statistical testing.....
2017-04-04 12:37:34,073 Start to run GSEA...Might take a while..................
2017-04-04 12:37:49,020 Start to generate gseapy reports, and produce figures...
2017-04-04 12:37:54,478 Congratulations...GSEAPY run successfully...............

In [13]:
mf_rt


Out[13]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0003723 0.497 2.713 0.000e+00 0.000e+00 367 51 [7655641, 64669875, 20323736, 33709212, 10185112, 5141220, 8283720, 17035162, 52960359, 5730052, 8974409, 23226729, 6962424, 15891127, 29630113, 23720124, 8107184, 26879329, 20132923, 16968363, 38183434, 40487328, 15916898, 5365520, 61892960, 3492858, 4100571, 10593880, 62224782, 41621220, 36697039, 61884939, 23721515, 38302786, 12493950, 30459755, 31342205, 33208200, 12690700, 10631876, 5753625, 68927583, 30556349, 65259195, 167619418, 65777235, 62322368, 10899352, 67968100, 29262834, 65669111] RNA binding
GO:0004618 0.644 2.616 0.000e+00 5.094e-05 78 19 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 33420375, 22187812, 67028544, 59725586, 54913980, 4220178, 168089107, 65935692, 62829929, 63123662] phosphoglycerate kinase activity
GO:0016774 0.582 2.472 0.000e+00 1.019e-04 111 22 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 33420375, 22187812, 67028544, 59725586, 54913980, 3884277, 4220178, 63123377, 168089107, 65935692, 62829929, 13604374, 63123662] phosphotransferase activity, carboxyl group as acceptor
GO:0001882 0.465 2.212 2.914e-04 2.623e-03 398 31 [5888442, 80382425, 10185112, 21138590, 69205977, 5730052, 8974409, 32794085, 12661961, 40640683, 12999155, 6243639, 23375966, 26879329, 4100571, 36454371, 61884939, 61982117, 49556056, 69572327, 61106614, 15782696, 5753625, 30556349, 80394470, 67719393, 15769577, 167619418, 40723118, 29262834, 3557492] nucleoside binding
GO:0016301 0.443 2.174 2.895e-04 3.199e-03 480 34 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 33420375, 22187812, 61635847, 67028544, 59725586, 54913980, 3884277, 17583418, 61708790, 4220178, 62102911, 63123377, 51371961, 36117032, 62942343, 48698283, 168089107, 65935692, 55261886, 48298182, 64346968, 62829929, 13604374, 62098267, 63123662] kinase activity
GO:0019001 0.449 2.064 1.937e-03 7.810e-03 248 28 [5888442, 80382425, 10185112, 21138590, 69205977, 5730052, 8974409, 32794085, 12661961, 40640683, 26879329, 4100571, 36454371, 61884939, 61982117, 49556056, 69572327, 61106614, 15782696, 5753625, 30556349, 80394470, 67719393, 15769577, 167619418, 40723118, 29262834, 3557492] guanyl nucleotide binding
GO:0001883 0.449 2.062 1.185e-03 6.782e-03 248 28 [5888442, 80382425, 10185112, 21138590, 69205977, 5730052, 8974409, 32794085, 12661961, 40640683, 26879329, 4100571, 36454371, 61884939, 61982117, 49556056, 69572327, 61106614, 15782696, 5753625, 30556349, 80394470, 67719393, 15769577, 167619418, 40723118, 29262834, 3557492] purine nucleoside binding
GO:0003735 0.334 1.963 1.743e-03 1.406e-02 360 65 [7655641, 64669875, 20323736, 33709212, 19107849, 29630217, 5141220, 8283720, 17035162, 5645650, 60453073, 165941560, 28829095, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 16968363, 38183434, 40487328, 15916898, 5365520, 3492858, 10593880, 62224782, 41621220, 36697039, 23449836, 23721515, 38302786, 12493950, 30459755, 31342205, 33208200, 12690700, 3576806, 68927583, 65259195, 65777235, 67911420, 39007615, 10899352, 64474525, 42272589, 66752541, 167990362, 68373997, 65506212, 65977068, 67968100, 33140401, 167623679, 65626218, 67383571, 38249992, 10276368, 65669111, 13581456, 166036375] structural constituent of ribosome
GO:0022892 0.504 1.875 6.516e-03 2.511e-02 89 15 [3885199, 1994037, 29978920, 33721585, 38210955, 54503535, 21357752, 32363526, 1809293, 268176, 21432496, 27807827, 62660497, 64582513, 165706474] substrate-specific transporter activity
GO:0000287 0.437 1.717 2.134e-02 6.799e-02 113 17 [29629717, 9654148, 23089117, 25933508, 17589318, 29001612, 27290903, 26904631, 29983272, 20853009, 7496609, 28314259, 63235820, 63648739, 63662802, 62176760, 62566960] magnesium ion binding

In [14]:
mf_control


Out[14]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0004553 -0.480 -1.767 0.018 0.345 75 11 [11310495, 11310502, 167639021, 61777171, 63376055, 63922748, 167549118, 62488243, 62521472, 13605039, 62450924] hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0016798 -0.480 -1.765 0.019 0.175 76 11 [11310495, 11310502, 167639021, 61777171, 63376055, 63922748, 167549118, 62488243, 62521472, 13605039, 62450924] hydrolase activity, acting on glycosyl bonds
GO:0050662 -0.328 -1.734 0.017 0.138 235 27 [29001612, 27290903, 26904631, 29983272, 20853009, 7496609, 6997781, 3740901, 15860346, 63640418, 20839749, 63296313, 63305114, 63379850, 62942791, 168109762, 63626599, 63235820, 61621955, 63648739, 63662802, 63389326, 61809381, 48540155, 21899103, 61608244, 166278783] coenzyme binding
GO:0009055 -0.541 -1.733 0.027 0.104 38 8 [63305114, 63379850, 62942791, 49911241, 63626599, 61957888, 63389326, 167701862] electron carrier activity
GO:0016903 -0.366 -1.589 0.048 0.173 282 16 [36107728, 6997781, 43414939, 3740901, 15860346, 10318713, 63640418, 61880488, 168109762, 61621955, 45723591, 62312164, 57098781, 21899103, 61608244, 166278783] oxidoreductase activity, acting on the aldehyde or oxo group of donors

In [15]:
bp_rt


Out[15]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0009132 0.408 2.117 8.412e-04 0.033 304 41 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 17046519, 5960044, 8200910, 65033516, 30588025, 64427981, 4220178, 62102911, 168089107, 65935692, 55261886, 48298182, 64346968, 62829929, 62566960, 64479173, 64978197, 62098267, 63123662] nucleoside diphosphate metabolic process
GO:0046939 0.408 2.113 8.461e-04 0.017 304 41 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 17046519, 5960044, 8200910, 65033516, 30588025, 64427981, 4220178, 62102911, 168089107, 65935692, 55261886, 48298182, 64346968, 62829929, 62566960, 64479173, 64978197, 62098267, 63123662] nucleotide phosphorylation
GO:0009135 0.408 2.111 9.901e-04 0.012 302 41 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 17046519, 5960044, 8200910, 65033516, 30588025, 64427981, 4220178, 62102911, 168089107, 65935692, 55261886, 48298182, 64346968, 62829929, 62566960, 64479173, 64978197, 62098267, 63123662] purine nucleoside diphosphate metabolic process
GO:0072524 0.401 2.091 7.072e-04 0.010 305 42 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 17046519, 5960044, 8200910, 65033516, 30588025, 64427981, 4220178, 62102911, 168089107, 65935692, 166574781, 55261886, 48298182, 64346968, 62829929, 62566960, 64479173, 64978197, 62098267, 63123662] pyridine-containing compound metabolic process
GO:0006733 0.401 2.089 7.050e-04 0.008 305 42 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 17046519, 5960044, 8200910, 65033516, 30588025, 64427981, 4220178, 62102911, 168089107, 65935692, 166574781, 55261886, 48298182, 64346968, 62829929, 62566960, 64479173, 64978197, 62098267, 63123662] oxidoreduction coenzyme metabolic process
GO:0044267 0.352 2.088 0.000e+00 0.007 413 69 [7655641, 64669875, 20323736, 33709212, 27212193, 38310093, 19107849, 29630217, 5141220, 8283720, 17035162, 5645650, 60453073, 165941560, 28829095, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 16968363, 38183434, 40487328, 15916898, 5365520, 3492858, 21157792, 10593880, 62224782, 41621220, 36697039, 23449836, 23721515, 38302786, 12493950, 30459755, 31342205, 33208200, 12690700, 3576806, 68927583, 65259195, 28150928, 65777235, 67911420, 39007615, 10899352, 64474525, 42272589, 66752541, 167990362, 68373997, 65506212, 65977068, 67968100, 33140401, 167623679, 65626218, 67383571, 38249992, 10276368, 65669111, 13581456, 166036375] cellular protein metabolic process
GO:0009141 0.392 2.087 5.639e-04 0.006 381 45 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 32363526, 1809293, 22187812, 268176, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 17046519, 5960044, 8200910, 65033516, 30588025, 64427981, 4220178, 62102911, 168089107, 65935692, 55261886, 48298182, 64346968, 62829929, 62566960, 64479173, 64978197, 62098267, 63123662] nucleoside triphosphate metabolic process
GO:0046034 0.392 2.086 1.533e-03 0.005 379 45 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 32363526, 1809293, 22187812, 268176, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 17046519, 5960044, 8200910, 65033516, 30588025, 64427981, 4220178, 62102911, 168089107, 65935692, 55261886, 48298182, 64346968, 62829929, 62566960, 64479173, 64978197, 62098267, 63123662] ATP metabolic process
GO:0009126 0.385 2.057 1.520e-03 0.007 409 46 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 32363526, 1809293, 22187812, 268176, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 17046519, 5960044, 8200910, 65033516, 30588025, 64427981, 4220178, 62102911, 168089107, 65935692, 55261886, 48298182, 64346968, 62829929, 62566960, 63180877, 64479173, 64978197, 62098267, 63123662] purine nucleoside monophosphate metabolic process
GO:0009123 0.385 2.045 1.260e-03 0.007 412 46 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 32363526, 1809293, 22187812, 268176, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 17046519, 5960044, 8200910, 65033516, 30588025, 64427981, 4220178, 62102911, 168089107, 65935692, 55261886, 48298182, 64346968, 62829929, 62566960, 63180877, 64479173, 64978197, 62098267, 63123662] nucleoside monophosphate metabolic process
GO:0006732 0.387 2.040 8.487e-04 0.006 391 44 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 17046519, 5960044, 8200910, 65033516, 30588025, 64427981, 4220178, 62102911, 168089107, 65935692, 61880488, 166574781, 55261886, 48298182, 64346968, 62829929, 62479129, 62566960, 64479173, 64978197, 62098267, 63123662] coenzyme metabolic process
GO:0051186 0.387 2.036 1.260e-03 0.006 413 44 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 17046519, 5960044, 8200910, 65033516, 30588025, 64427981, 4220178, 62102911, 168089107, 65935692, 61880488, 166574781, 55261886, 48298182, 64346968, 62829929, 62479129, 62566960, 64479173, 64978197, 62098267, 63123662] cofactor metabolic process
GO:0009259 0.376 2.036 1.815e-03 0.005 414 47 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 32363526, 1809293, 22187812, 268176, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 17046519, 5960044, 8200910, 65033516, 30588025, 64427981, 4220178, 62102911, 168089107, 65935692, 55261886, 48298182, 64346968, 62829929, 62566960, 63180877, 62356804, 64479173, 64978197, 62098267, 63123662] ribonucleotide metabolic process
GO:0072521 0.376 2.031 1.538e-03 0.005 475 47 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 32363526, 1809293, 22187812, 268176, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 17046519, 5960044, 8200910, 65033516, 30588025, 64427981, 4220178, 62102911, 168089107, 65935692, 55261886, 48298182, 64346968, 62829929, 62566960, 63180877, 62356804, 64479173, 64978197, 62098267, 63123662] purine-containing compound metabolic process
GO:0019693 0.376 2.015 1.106e-03 0.006 416 47 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 32363526, 1809293, 22187812, 268176, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 17046519, 5960044, 8200910, 65033516, 30588025, 64427981, 4220178, 62102911, 168089107, 65935692, 55261886, 48298182, 64346968, 62829929, 62566960, 63180877, 62356804, 64479173, 64978197, 62098267, 63123662] ribose phosphate metabolic process
GO:0009150 0.376 2.015 1.118e-03 0.005 412 47 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 32363526, 1809293, 22187812, 268176, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 17046519, 5960044, 8200910, 65033516, 30588025, 64427981, 4220178, 62102911, 168089107, 65935692, 55261886, 48298182, 64346968, 62829929, 62566960, 63180877, 62356804, 64479173, 64978197, 62098267, 63123662] purine ribonucleotide metabolic process
GO:0016052 0.369 2.007 1.242e-03 0.006 339 48 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 4715355, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 61635847, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 17046519, 5960044, 8200910, 65033516, 30588025, 64427981, 4220178, 62102911, 168089107, 65935692, 62445847, 63332989, 55261886, 48298182, 64346968, 62829929, 62566960, 62216988, 64479173, 64978197, 13605039, 62098267, 62450924, 63123662] carbohydrate catabolic process
GO:0044724 0.369 1.983 1.659e-03 0.007 336 48 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 4715355, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 61635847, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 17046519, 5960044, 8200910, 65033516, 30588025, 64427981, 4220178, 62102911, 168089107, 65935692, 62445847, 63332989, 55261886, 48298182, 64346968, 62829929, 62566960, 62216988, 64479173, 64978197, 13605039, 62098267, 62450924, 63123662] single-organism carbohydrate catabolic process
GO:0006518 0.334 1.972 1.348e-03 0.007 378 65 [7655641, 64669875, 20323736, 33709212, 19107849, 29630217, 5141220, 8283720, 17035162, 5645650, 60453073, 165941560, 28829095, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 16968363, 38183434, 40487328, 15916898, 5365520, 3492858, 10593880, 62224782, 41621220, 36697039, 23449836, 23721515, 38302786, 12493950, 30459755, 31342205, 33208200, 12690700, 3576806, 68927583, 65259195, 65777235, 67911420, 39007615, 10899352, 64474525, 42272589, 66752541, 167990362, 68373997, 65506212, 65977068, 67968100, 33140401, 167623679, 65626218, 67383571, 38249992, 10276368, 65669111, 13581456, 166036375] peptide metabolic process
GO:0043603 0.334 1.957 2.534e-03 0.007 414 65 [7655641, 64669875, 20323736, 33709212, 19107849, 29630217, 5141220, 8283720, 17035162, 5645650, 60453073, 165941560, 28829095, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 16968363, 38183434, 40487328, 15916898, 5365520, 3492858, 10593880, 62224782, 41621220, 36697039, 23449836, 23721515, 38302786, 12493950, 30459755, 31342205, 33208200, 12690700, 3576806, 68927583, 65259195, 65777235, 67911420, 39007615, 10899352, 64474525, 42272589, 66752541, 167990362, 68373997, 65506212, 65977068, 67968100, 33140401, 167623679, 65626218, 67383571, 38249992, 10276368, 65669111, 13581456, 166036375] cellular amide metabolic process
GO:0009117 0.356 1.954 2.497e-03 0.007 496 50 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 32363526, 1809293, 22187812, 268176, 63441836, 67028544, 19508028, 59725586, 54913980, 30623941, 839701, 12964871, 21164095, 17046519, 5960044, 8200910, 65033516, 30588025, 64427981, 4220178, 62102911, 168089107, 65935692, 166574781, 55261886, 48298182, 64346968, 62829929, 62566960, 63180877, 62356804, 64479173, 64978197, 62098267, 63123662] nucleotide metabolic process
GO:0043043 0.334 1.953 2.278e-03 0.007 377 65 [7655641, 64669875, 20323736, 33709212, 19107849, 29630217, 5141220, 8283720, 17035162, 5645650, 60453073, 165941560, 28829095, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 16968363, 38183434, 40487328, 15916898, 5365520, 3492858, 10593880, 62224782, 41621220, 36697039, 23449836, 23721515, 38302786, 12493950, 30459755, 31342205, 33208200, 12690700, 3576806, 68927583, 65259195, 65777235, 67911420, 39007615, 10899352, 64474525, 42272589, 66752541, 167990362, 68373997, 65506212, 65977068, 67968100, 33140401, 167623679, 65626218, 67383571, 38249992, 10276368, 65669111, 13581456, 166036375] peptide biosynthetic process
GO:0006753 0.356 1.947 2.204e-03 0.007 497 50 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 32363526, 1809293, 22187812, 268176, 63441836, 67028544, 19508028, 59725586, 54913980, 30623941, 839701, 12964871, 21164095, 17046519, 5960044, 8200910, 65033516, 30588025, 64427981, 4220178, 62102911, 168089107, 65935692, 166574781, 55261886, 48298182, 64346968, 62829929, 62566960, 63180877, 62356804, 64479173, 64978197, 62098267, 63123662] nucleoside phosphate metabolic process
GO:0043604 0.334 1.945 1.608e-03 0.007 411 65 [7655641, 64669875, 20323736, 33709212, 19107849, 29630217, 5141220, 8283720, 17035162, 5645650, 60453073, 165941560, 28829095, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 16968363, 38183434, 40487328, 15916898, 5365520, 3492858, 10593880, 62224782, 41621220, 36697039, 23449836, 23721515, 38302786, 12493950, 30459755, 31342205, 33208200, 12690700, 3576806, 68927583, 65259195, 65777235, 67911420, 39007615, 10899352, 64474525, 42272589, 66752541, 167990362, 68373997, 65506212, 65977068, 67968100, 33140401, 167623679, 65626218, 67383571, 38249992, 10276368, 65669111, 13581456, 166036375] amide biosynthetic process
GO:0006412 0.334 1.938 2.150e-03 0.007 372 65 [7655641, 64669875, 20323736, 33709212, 19107849, 29630217, 5141220, 8283720, 17035162, 5645650, 60453073, 165941560, 28829095, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 16968363, 38183434, 40487328, 15916898, 5365520, 3492858, 10593880, 62224782, 41621220, 36697039, 23449836, 23721515, 38302786, 12493950, 30459755, 31342205, 33208200, 12690700, 3576806, 68927583, 65259195, 65777235, 67911420, 39007615, 10899352, 64474525, 42272589, 66752541, 167990362, 68373997, 65506212, 65977068, 67968100, 33140401, 167623679, 65626218, 67383571, 38249992, 10276368, 65669111, 13581456, 166036375] translation
GO:0044712 0.347 1.908 4.448e-03 0.009 355 51 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 4715355, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 61635847, 67028544, 19508028, 59725586, 54913980, 30623941, 839701, 12964871, 21164095, 17046519, 5960044, 8200910, 65033516, 30588025, 64427981, 4220178, 62102911, 168089107, 65935692, 62445847, 63332989, 55261886, 48298182, 64346968, 62829929, 62566960, 13604025, 62216988, 64479173, 64978197, 13605039, 62098267, 62450924, 63123662] single-organism catabolic process
GO:0006091 0.352 1.907 2.895e-03 0.008 474 48 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 18275642, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 17046519, 5960044, 8200910, 65033516, 30588025, 64427981, 4220178, 64395219, 13570629, 62102911, 168089107, 65935692, 168109762, 61621955, 55261886, 48298182, 64346968, 62829929, 62566960, 64479173, 64978197, 62098267, 63123662, 61608244, 166278783] generation of precursor metabolites and energy
GO:1901135 0.347 1.894 3.748e-03 0.009 447 51 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 32363526, 1809293, 22187812, 268176, 63441836, 61635847, 67028544, 19508028, 59725586, 54913980, 30623941, 839701, 12964871, 21164095, 17046519, 5960044, 8200910, 65033516, 30588025, 64427981, 4220178, 62102911, 168089107, 65935692, 55261886, 48298182, 64346968, 62829929, 62566960, 51262100, 63180877, 62356804, 64479173, 64978197, 62098267, 63123662] carbohydrate derivative metabolic process
GO:0009056 0.334 1.859 5.626e-03 0.011 409 53 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4737261, 4559493, 45207415, 4715355, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 61892960, 61635847, 67028544, 19508028, 59725586, 54913980, 30623941, 839701, 12964871, 21164095, 17046519, 5960044, 8200910, 65033516, 10631876, 30588025, 64427981, 4220178, 62102911, 168089107, 65935692, 62445847, 63332989, 55261886, 48298182, 64346968, 62829929, 62566960, 13604025, 62216988, 64479173, 64978197, 13605039, 62098267, 62450924, 63123662] catabolic process
GO:0019538 0.306 1.844 3.827e-03 0.012 478 75 [7655641, 64669875, 20323736, 33709212, 27212193, 38310093, 19107849, 29630217, 5141220, 8283720, 17035162, 5645650, 60453073, 165941560, 28829095, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 16968363, 38183434, 40487328, 15916898, 5365520, 3492858, 21157792, 10593880, 62224782, 41621220, 36697039, 23449836, 23721515, 38302786, 12493950, 30459755, 31342205, 33208200, 12690700, 3576806, 68927583, 65259195, 28150928, 62403068, 13571532, 65777235, 67911420, 39007615, 167394958, 10899352, 64474525, 42272589, 12417159, 66752541, 167990362, 41253846, 68373997, 65506212, 65977068, 67968100, 33140401, 167623679, 65626218, 67383571, 38249992, 10276368, 65669111, 13581456, 65232781, 166036375] protein metabolic process
GO:0072350 0.583 1.725 1.932e-02 0.029 29 8 [13684061, 78477008, 80889105, 26904631, 29983272, 20853009, 7496609, 3740901] tricarboxylic acid metabolic process
GO:0046364 0.529 1.705 2.190e-02 0.032 107 10 [36454371, 839701, 12964871, 61982117, 17046519, 5960044, 8200910, 65033516, 61106614, 45349478] monosaccharide biosynthetic process
GO:0043648 0.541 1.670 2.810e-02 0.038 43 9 [13684061, 6155443, 11147909, 16967630, 21276719, 56134344, 16965587, 51115316, 61809381] dicarboxylic acid metabolic process
GO:1902578 0.408 1.598 4.712e-02 0.059 132 17 [3885199, 1994037, 29978920, 33721585, 38210955, 54503535, 21357752, 32363526, 1809293, 268176, 21432496, 29629513, 27807827, 62660497, 64582513, 165706474, 67703402] single-organism localization
GO:0005996 0.348 1.584 4.156e-02 0.062 222 27 [4715355, 80888632, 10226000, 30252792, 61635847, 8532970, 36454371, 839701, 12964871, 6997781, 61982117, 17046519, 5960044, 8200910, 65033516, 17583418, 61106614, 166487064, 15860346, 63640418, 62199335, 45349478, 62299040, 62445847, 55848589, 21899103, 62216988] monosaccharide metabolic process

In [16]:
bp_control


Out[16]:
es nes pval fdr gene_set_size matched_size genes name
Term

In [17]:
cc_rt


Out[17]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0015934 0.660 2.114 6.653e-04 0.012 63 10 [7655641, 64669875, 20323736, 33709212, 8283720, 17035162, 15891127, 41621220, 10899352, 38249992] large ribosomal subunit
GO:0044444 0.335 2.014 1.710e-03 0.015 422 70 [7655641, 64669875, 20323736, 33709212, 29629717, 19107849, 29630217, 5141220, 8283720, 17035162, 23089117, 5645650, 60453073, 165941560, 28829095, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 16968363, 38183434, 40487328, 15916898, 5365520, 3492858, 80889105, 10593880, 62224782, 41621220, 36697039, 23449836, 23721515, 38302786, 12493950, 30459755, 31342205, 33208200, 12690700, 3576806, 68927583, 65259195, 65777235, 67911420, 39007615, 10899352, 64474525, 42272589, 66752541, 167990362, 68373997, 65506212, 65977068, 67968100, 33140401, 61809381, 167623679, 65626218, 62566960, 67383571, 38249992, 10276368, 65669111, 13581456, 166036375] cytoplasmic part
GO:0044446 0.491 1.988 2.516e-03 0.013 169 19 [7655641, 64669875, 20323736, 33709212, 8283720, 17035162, 23226729, 6962424, 15891127, 6288540, 20132923, 3492858, 10593880, 41621220, 68927583, 65259195, 10899352, 38249992, 65669111] intracellular organelle part
GO:0044391 0.491 1.987 1.997e-03 0.010 159 19 [7655641, 64669875, 20323736, 33709212, 8283720, 17035162, 23226729, 6962424, 15891127, 6288540, 20132923, 3492858, 10593880, 41621220, 68927583, 65259195, 10899352, 38249992, 65669111] ribosomal subunit
GO:1990904 0.334 1.952 2.281e-03 0.010 360 65 [7655641, 64669875, 20323736, 33709212, 19107849, 29630217, 5141220, 8283720, 17035162, 5645650, 60453073, 165941560, 28829095, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 16968363, 38183434, 40487328, 15916898, 5365520, 3492858, 10593880, 62224782, 41621220, 36697039, 23449836, 23721515, 38302786, 12493950, 30459755, 31342205, 33208200, 12690700, 3576806, 68927583, 65259195, 65777235, 67911420, 39007615, 10899352, 64474525, 42272589, 66752541, 167990362, 68373997, 65506212, 65977068, 67968100, 33140401, 167623679, 65626218, 67383571, 38249992, 10276368, 65669111, 13581456, 166036375] ribonucleoprotein complex
GO:0005622 0.377 1.932 3.536e-03 0.010 306 41 [7655641, 64669875, 20323736, 33709212, 19107849, 29630217, 10185112, 5141220, 5645650, 60453073, 5730052, 8974409, 165941560, 28829095, 25902959, 20862748, 15891127, 26879329, 4100571, 41621220, 3884277, 23449836, 61884939, 3576806, 5753625, 30556349, 65259195, 167619418, 63123377, 10899352, 64474525, 42272589, 68373997, 67968100, 33140401, 67383571, 38249992, 29262834, 10276368, 65669111, 13604374] intracellular
GO:0043232 0.312 1.764 1.199e-02 0.031 320 57 [7655641, 64669875, 20323736, 33709212, 19107849, 29630217, 5141220, 5645650, 60453073, 165941560, 28829095, 25902959, 20862748, 15891127, 29630113, 23720124, 8107184, 16968363, 38183434, 40487328, 15916898, 5365520, 3492858, 10593880, 62224782, 41621220, 36697039, 23449836, 23721515, 38302786, 12493950, 30459755, 31342205, 33208200, 12690700, 3576806, 68927583, 65777235, 67911420, 39007615, 10899352, 64474525, 42272589, 66752541, 167990362, 68373997, 65506212, 65977068, 67968100, 33140401, 167623679, 65626218, 67383571, 38249992, 10276368, 13581456, 166036375] intracellular non-membrane-bounded organelle
GO:0005840 0.312 1.762 1.024e-02 0.028 319 57 [7655641, 64669875, 20323736, 33709212, 19107849, 29630217, 5141220, 5645650, 60453073, 165941560, 28829095, 25902959, 20862748, 15891127, 29630113, 23720124, 8107184, 16968363, 38183434, 40487328, 15916898, 5365520, 3492858, 10593880, 62224782, 41621220, 36697039, 23449836, 23721515, 38302786, 12493950, 30459755, 31342205, 33208200, 12690700, 3576806, 68927583, 65777235, 67911420, 39007615, 10899352, 64474525, 42272589, 66752541, 167990362, 68373997, 65506212, 65977068, 67968100, 33140401, 167623679, 65626218, 67383571, 38249992, 10276368, 13581456, 166036375] ribosome
GO:0043229 0.312 1.758 9.684e-03 0.025 327 57 [7655641, 64669875, 20323736, 33709212, 19107849, 29630217, 5141220, 5645650, 60453073, 165941560, 28829095, 25902959, 20862748, 15891127, 29630113, 23720124, 8107184, 16968363, 38183434, 40487328, 15916898, 5365520, 3492858, 10593880, 62224782, 41621220, 36697039, 23449836, 23721515, 38302786, 12493950, 30459755, 31342205, 33208200, 12690700, 3576806, 68927583, 65777235, 67911420, 39007615, 10899352, 64474525, 42272589, 66752541, 167990362, 68373997, 65506212, 65977068, 67968100, 33140401, 167623679, 65626218, 67383571, 38249992, 10276368, 13581456, 166036375] intracellular organelle
GO:0044422 0.374 1.650 2.639e-02 0.045 402 25 [7655641, 64669875, 20323736, 33709212, 8283720, 17035162, 23226729, 6962424, 15891127, 6288540, 20132923, 3492858, 10593880, 41621220, 167307068, 13580518, 68927583, 65259195, 10899352, 168185530, 168106741, 166250719, 168173199, 38249992, 65669111] organelle part

In [18]:
cc_control


Out[18]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0016020 -0.466 -1.946 0.007 0.043 75 15 [21357752, 21687303, 167156307, 61699598, 166632550, 64013758, 61660751, 62830069, 62660497, 61957888, 166216926, 166593522, 167701862, 27635679, 165685567] membrane
GO:0043190 -0.527 -1.786 0.021 0.061 115 9 [63132923, 47513944, 11992086, 56076521, 17618404, 10265600, 37969849, 63374013, 28273397] ATP-binding cassette (ABC) transporter complex
GO:0098797 -0.527 -1.770 0.018 0.045 117 9 [63132923, 47513944, 11992086, 56076521, 17618404, 10265600, 37969849, 63374013, 28273397] plasma membrane protein complex
GO:0044459 -0.527 -1.770 0.024 0.034 119 9 [63132923, 47513944, 11992086, 56076521, 17618404, 10265600, 37969849, 63374013, 28273397] plasma membrane part
GO:1904949 -0.527 -1.767 0.019 0.027 117 9 [63132923, 47513944, 11992086, 56076521, 17618404, 10265600, 37969849, 63374013, 28273397] ATPase complex
GO:1990351 -0.527 -1.766 0.021 0.023 117 9 [63132923, 47513944, 11992086, 56076521, 17618404, 10265600, 37969849, 63374013, 28273397] transporter complex

Rag vs WT Human/Mouse


In [19]:
out_dir = "Rag_WT_hm_gsea"
df = pd.read_csv(os.path.join(BASE,"Rag_WT_results_named_annot.csv"))
df = df[(df.padj.abs()<=0.2)]
df = df[df.human_mouse]
df['log2FoldChange'] = -1 * df['log2FoldChange']
rank_df = df[['Unnamed: 0', 'log2FoldChange']].rename(columns={'Unnamed: 0': 'gene_name', 'log2FoldChange': 'rank'})
rank_df = rank_df.sort_values('rank').reset_index(drop=True)
mf_res = run_go_gsea(rank_df, mf_map_f, seed=1111, outdir=out_dir)
bp_res = run_go_gsea(rank_df, bp_map_f, seed=1111, outdir=out_dir)
#cc_res = run_go_gsea(rank_df, cc_map_f, seed=1111, outdir=out_dir)
mf_rag = mf_res.query('nes > 0 and pval < 0.05').sort_values('nes', ascending=False)
mf_wt = mf_res.query('nes < 0 and pval < 0.05').sort_values('nes', ascending=True)
bp_rag = bp_res.query('nes > 0 and pval < 0.05').sort_values('nes', ascending=False)
bp_wt = bp_res.query('nes < 0 and pval < 0.05').sort_values('nes', ascending=True)
#cc_rt = cc_res.query('nes > 0 and pval < 0.05').sort_values('nes', ascending=False)
#cc_control = cc_res.query('nes < 0 and pval < 0.05').sort_values('nes', ascending=True)


2017-04-04 12:37:54,857 Parsing data files for GSEA.............................
/usr/lib/python3/dist-packages/numpy/lib/arraysetops.py:379: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
  mask |= (ar1 == a)
2017-04-04 12:37:54,889 0004 gene_sets used for further statistical testing.....
2017-04-04 12:37:54,890 Start to run GSEA...Might take a while..................
2017-04-04 12:37:55,244 Start to generate gseapy reports, and produce figures...
/usr/lib/python3/dist-packages/matplotlib/figure.py:1744: UserWarning: This figure includes Axes that are not compatible with tight_layout, so its results might be incorrect.
  warnings.warn("This figure includes Axes that are not "
2017-04-04 12:37:56,299 Congratulations...GSEAPY run successfully...............
2017-04-04 12:37:56,315 Parsing data files for GSEA.............................
2017-04-04 12:37:56,354 0004 gene_sets used for further statistical testing.....
2017-04-04 12:37:56,355 Start to run GSEA...Might take a while..................
2017-04-04 12:37:56,862 Start to generate gseapy reports, and produce figures...
2017-04-04 12:37:58,092 Congratulations...GSEAPY run successfully...............

In [20]:
mf_rag


Out[20]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0046872 0.531 1.679 0.028 0.087 488 9 [61501076, 61502914, 61500363, 61501312, 61499612, 165666724, 61499523, 61495726, 165637224] metal ion binding

In [21]:
mf_wt


Out[21]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0005515 -0.864 -1.869 1.363e-04 6.931e-04 108 6 [165662997, 61499944, 165642270, 165664161, 165646313, 165661842] protein binding

In [22]:
bp_rag


Out[22]:
es nes pval fdr gene_set_size matched_size genes name
Term

In [23]:
bp_wt


Out[23]:
es nes pval fdr gene_set_size matched_size genes name
Term

Rag vs WT Non-Human/Mouse


In [24]:
out_dir = "Rag_WT_gsea"
df = pd.read_csv(os.path.join(BASE,"Rag_WT_results_named_annot.csv"))
df = df[(df.padj.abs()<=0.2)]
df = df[~df.human_mouse]
df['log2FoldChange'] = -1 * df['log2FoldChange']
rank_df = df[['Unnamed: 0', 'log2FoldChange']].rename(columns={'Unnamed: 0': 'gene_name', 'log2FoldChange': 'rank'})
rank_df = rank_df.sort_values('rank').reset_index(drop=True)

In [25]:
mf_res = run_go_gsea(rank_df, mf_map_f, seed=1111, outdir=out_dir)
bp_res = run_go_gsea(rank_df, bp_map_f, seed=1111, outdir=out_dir)
cc_res = run_go_gsea(rank_df, cc_map_f, seed=1111, outdir=out_dir)
mf_rag = mf_res.query('nes > 0 and pval < 0.05').sort_values('nes', ascending=False)
mf_wt = mf_res.query('nes < 0 and pval < 0.05').sort_values('nes', ascending=True)
bp_rag = bp_res.query('nes > 0 and pval < 0.05').sort_values('nes', ascending=False)
bp_wt = bp_res.query('nes < 0 and pval < 0.05').sort_values('nes', ascending=True)
cc_rag = cc_res.query('nes > 0 and pval < 0.05').sort_values('nes', ascending=False)
cc_wt = cc_res.query('nes < 0 and pval < 0.05').sort_values('nes', ascending=True)


2017-04-04 12:37:58,412 Parsing data files for GSEA.............................
/usr/lib/python3/dist-packages/numpy/lib/arraysetops.py:379: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
  mask |= (ar1 == a)
2017-04-04 12:37:58,798 0074 gene_sets used for further statistical testing.....
2017-04-04 12:37:58,799 Start to run GSEA...Might take a while..................
2017-04-04 12:40:36,547 Start to generate gseapy reports, and produce figures...
/usr/lib/python3/dist-packages/matplotlib/figure.py:1744: UserWarning: This figure includes Axes that are not compatible with tight_layout, so its results might be incorrect.
  warnings.warn("This figure includes Axes that are not "
2017-04-04 12:40:42,654 Congratulations...GSEAPY run successfully...............
2017-04-04 12:40:42,670 Parsing data files for GSEA.............................
2017-04-04 12:40:43,051 0103 gene_sets used for further statistical testing.....
2017-04-04 12:40:43,052 Start to run GSEA...Might take a while..................
2017-04-04 12:44:17,867 Start to generate gseapy reports, and produce figures...
2017-04-04 12:44:23,888 Congratulations...GSEAPY run successfully...............
2017-04-04 12:44:23,895 Parsing data files for GSEA.............................
2017-04-04 12:44:23,973 0026 gene_sets used for further statistical testing.....
2017-04-04 12:44:23,975 Start to run GSEA...Might take a while..................
2017-04-04 12:45:17,584 Start to generate gseapy reports, and produce figures...
2017-04-04 12:45:23,505 Congratulations...GSEAPY run successfully...............

In [26]:
mf_rag


Out[26]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0016903 0.427 2.458 0.000e+00 1.541e-04 282 75 [57377692, 57602627, 20987406, 10318713, 61599909, 63509022, 6997781, 166781730, 44171740, 61901179, 64549605, 61599853, 61601993, 61717636, 61880488, 53586382, 63603065, 39787404, 63849179, 166052469, 50431192, 166155431, 61033726, 61686088, 6574706, 61986126, 52336699, 61603708, 63571991, 57894284, 58687019, 62139539, 52783963, 168109762, 59329815, 63900260, 61600015, 61963309, 61600538, 166304100, 64211477, 66913607, 60255223, 44281203, 62141702, 41869870, 63007267, 52484917, 64109059, 53437685, 55526608, 47654592, 37964574, 10739365, 50135248, 64872068, 167530105, 62669104, 49924705, 62232545, 20607209, 62943474, 61598699, 63032818, 61588102, 57566721, 62151332, 45794851, 40525078, 54342385, 45816831, 53596244, 63371685, 40636025, 63600850] oxidoreductase activity, acting on the aldehyde or oxo group of donors
GO:0009055 0.730 2.457 0.000e+00 7.706e-05 38 12 [63098496, 64646230, 21834593, 6263025, 63079626, 62114668, 11316432, 47763199, 11316431, 167701862, 64864375, 63507869] electron carrier activity
GO:0051540 0.479 2.329 0.000e+00 4.110e-04 149 38 [62751142, 63901915, 167744672, 62114668, 28421698, 57377692, 57602627, 20987406, 61599909, 63509022, 64549605, 61599853, 61601993, 167701862, 39787404, 166052469, 61603708, 58687019, 62139539, 168109762, 61600015, 61963309, 61600538, 166304100, 64211477, 27694381, 60255223, 62141702, 64109059, 50135248, 49924705, 20607209, 61598699, 61588102, 62151332, 45794851, 54342385, 45816831] metal cluster binding
GO:0016820 0.460 2.183 1.898e-04 2.138e-03 190 35 [62344870, 168161151, 28240379, 40674602, 62545344, 62072713, 21258712, 165851092, 63132923, 65516796, 66978191, 31357673, 32955361, 40686252, 13203808, 32157942, 13841186, 6347838, 12378604, 8187004, 62946388, 6934942, 47513944, 37969849, 63199719, 10732421, 27603383, 62055617, 33383613, 62354250, 65627086, 63129880, 61865720, 63078357, 13568664] hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances
GO:0016868 0.613 2.061 1.738e-03 5.379e-03 79 12 [167401290, 39279903, 62071220, 168126288, 41534199, 8102980, 53821637, 38613059, 67730070, 62143029, 42049385, 62198791] intramolecular transferase activity, phosphotransferases
GO:0016866 0.613 2.041 2.309e-03 5.381e-03 112 12 [167401290, 39279903, 62071220, 168126288, 41534199, 8102980, 53821637, 38613059, 67730070, 62143029, 42049385, 62198791] intramolecular transferase activity
GO:0022804 0.426 2.033 1.715e-03 5.075e-03 205 36 [62344870, 168161151, 28240379, 40674602, 62545344, 62072713, 21258712, 165851092, 63132923, 65516796, 66978191, 31357673, 32955361, 40686252, 13203808, 32157942, 13841186, 6347838, 12378604, 8187004, 62946388, 6934942, 47513944, 37969849, 63199719, 10732421, 27603383, 62055617, 33383613, 62354250, 65627086, 63129880, 61865720, 63078357, 165706474, 13568664] active transmembrane transporter activity
GO:0016620 0.433 1.951 1.539e-03 9.536e-03 101 30 [10318713, 6997781, 166781730, 44171740, 61717636, 53586382, 50431192, 166155431, 61033726, 61686088, 6574706, 61986126, 52336699, 63571991, 57894284, 52783963, 66913607, 44281203, 41869870, 63007267, 52484917, 53437685, 55526608, 47654592, 10739365, 167530105, 62943474, 63032818, 63371685, 63600850] oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
GO:0022857 0.384 1.849 4.042e-03 1.968e-02 212 37 [62344870, 168161151, 28240379, 40674602, 62545344, 62072713, 21258712, 165851092, 63132923, 65516796, 66978191, 31357673, 32955361, 40686252, 13203808, 32157942, 13841186, 6347838, 12378604, 8187004, 62946388, 6934942, 47513944, 37969849, 63199719, 10732421, 27603383, 62055617, 33383613, 62354250, 65627086, 63129880, 61865720, 63078357, 165706474, 64582513, 13568664] transmembrane transporter activity
GO:0050660 0.543 1.817 1.345e-02 2.266e-02 43 12 [7011122, 166616289, 62304018, 63105175, 11316432, 165961991, 22084793, 64864375, 63507869, 60375800, 64117322, 62289912] flavin adenine dinucleotide binding
GO:0005215 0.322 1.735 6.581e-03 3.709e-02 256 57 [167285315, 13587543, 167348034, 165992613, 167399046, 21799059, 62047389, 62623865, 166635414, 168124343, 11412988, 62344870, 28423332, 168161151, 63070669, 166208277, 28240379, 40674602, 62545344, 62072713, 21258712, 165851092, 63132923, 65516796, 66978191, 31357673, 32955361, 40686252, 13203808, 32157942, 13841186, 6347838, 12378604, 8187004, 62946388, 6934942, 47513944, 37969849, 63199719, 10732421, 27603383, 62055617, 33383613, 62354250, 65627086, 63129880, 61865720, 63078357, 165706474, 13570595, 167606365, 64582513, 165776049, 13568664, 4019294, 167556744, 65386242] transporter activity
GO:0050662 0.321 1.723 1.107e-02 3.670e-02 235 54 [7011122, 166616289, 62304018, 62720663, 63105175, 63228299, 63334059, 11316432, 63236804, 63863560, 63958498, 57602627, 20987406, 63236003, 63403045, 165961991, 166389161, 56135140, 6997781, 61599853, 61601993, 22084793, 11307495, 64328599, 61603708, 168109762, 61600015, 61600538, 62141702, 64864375, 20607209, 63507869, 62943474, 61598699, 63032818, 61588102, 54342385, 60375800, 63371685, 22083024, 10530122, 62737033, 64587749, 63158778, 62853917, 63677227, 10822577, 54615426, 61965999, 21360480, 64117322, 63600850, 61809381, 62289912] coenzyme binding
GO:0048037 0.272 1.688 6.192e-03 4.283e-02 388 102 [7011122, 166616289, 62304018, 62720663, 63098496, 21834593, 63105175, 6263025, 63079626, 63228299, 28421698, 63334059, 11316432, 27696183, 21808882, 63236804, 63863560, 63958498, 22351058, 168075980, 62743829, 57602627, 20987406, 63236003, 61703706, 63403045, 165961991, 166389161, 56135140, 62783884, 63323004, 6997781, 37010279, 167595271, 61599853, 166632550, 61601993, 22084793, 77096042, 11307495, 64328599, 62084319, 61603708, 168109762, 61600015, 61600538, 62141702, 61748514, 64864375, 20607209, 63507869, 62943474, 61598699, 63032818, 165689798, 61588102, 22197112, 61742431, 63286685, 54342385, 60375800, 62948337, 66510411, 49462236, 62718756, 63371685, 61756955, 51344941, 30290988, 40544251, 66822118, 62207461, 37568190, 22083024, 12023663, 65099450, 39202078, 56071476, 51146942, 10530122, 62652073, 62737033, 64587749, 63158778, 63013915, 62853917, 63677227, 10822577, 54615426, 61965999, 21360480, 62284246, 64117322, 63600850, 52250379, 44274395, 63055945, 61809381, 63086724, 62289912, ...] cofactor binding
GO:0016746 0.363 1.644 2.045e-02 5.231e-02 95 31 [58064589, 40137855, 65878597, 44862322, 42607851, 62936292, 66019300, 63846694, 57658806, 46814695, 62315214, 166039238, 54925585, 36145840, 62410329, 20753284, 4416550, 62898460, 57699664, 59943276, 57876845, 44334817, 27671912, 43152722, 62714759, 62637752, 1488186, 28669161, 61809381, 62853510, 64167079] transferase activity, transferring acyl groups
GO:0016773 0.358 1.618 2.937e-02 5.679e-02 113 30 [21799656, 62247377, 21828249, 66146520, 64412215, 167526299, 62422222, 165866251, 52517748, 45069464, 40885240, 41505027, 13753597, 45247619, 63185681, 41087706, 45919266, 62560655, 166007049, 8551124, 62952131, 165706474, 166287375, 13567160, 13588358, 52333023, 59827295, 65218941, 28234013, 62109485] phosphotransferase activity, alcohol group as acceptor
GO:0046914 0.311 1.564 2.930e-02 7.259e-02 257 45 [62114668, 4416015, 62515931, 61599909, 64549605, 61599853, 61601993, 22084793, 47787704, 166165052, 63157973, 65999129, 61603708, 168109762, 64182902, 63865771, 61600015, 61963309, 61600538, 166304100, 64211477, 27694381, 65586747, 60255223, 64109059, 37964574, 50135248, 49924705, 18213545, 62232545, 63272810, 29774394, 63649356, 20607209, 61598699, 63517822, 61588102, 63973174, 37345174, 64823101, 67497751, 46312448, 40859402, 42863898, 61809381] transition metal ion binding
GO:0016853 0.303 1.564 3.068e-02 6.850e-02 288 48 [27618367, 167401290, 63228299, 39279903, 63334059, 167473156, 63236804, 167029093, 63236003, 63403045, 166389161, 64711323, 64328599, 18134535, 64380885, 62071220, 53022688, 168126288, 20752463, 41534199, 8102980, 53821637, 38613059, 69926951, 67730070, 62661009, 62143029, 32079045, 42049385, 18950035, 62198791, 54139955, 54193303, 62446788, 62445847, 62405280, 62299040, 64823101, 62636935, 22197670, 50712297, 65812454, 65380227, 58900609, 10530122, 11404724, 61950988, 6131330] isomerase activity

In [27]:
mf_wt


Out[27]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0097747 -0.653 -4.453 0.000e+00 0.000e+00 345 143 [61571198, 61950469, 47461425, 15059448, 8291718, 17558356, 7937195, 15768925, 9047445, 6340712, 10774345, 10795597, 20809021, 48701865, 51091566, 41242615, 37208030, 42830626, 21296655, 61588900, 60772420, 56745534, 50065172, 62167253, 44186767, 167412647, 61599553, 17559280, 30840365, 6056719, 6023174, 14700148, 10699458, 7440434, 5830788, 16830531, 36374512, 12803565, 22055143, 27851830, 166882954, 43146673, 21868198, 61079203, 61952789, 7691951, 21252862, 50058218, 27880167, 61604840, 22236358, 61597374, 61579823, 45428002, 58926833, 63555859, 62326869, 39588863, 61605755, 40887919, 61597571, 61601524, 14167279, 24340641, 21966233, 21075844, 61580012, 61580937, 18214391, 9670834, 61573275, 8305836, 61669421, 61603176, 61601759, 7435501, 56735007, 65613889, 63632220, 58090628, 30077373, 26013941, 44284503, 66863306, 63185291, 41171397, 45190220, 21909748, 63027032, 62634255, 20706901, 62427434, 58137973, 62092597, 59642867, 37935841, 62130826, 38315748, 58701908, 41204377, ...] RNA polymerase activity
GO:0016779 -0.614 -4.359 0.000e+00 0.000e+00 463 171 [18523127, 28436439, 40551040, 59156012, 63039326, 57028376, 65657046, 63112646, 38175368, 62718684, 27804972, 61571198, 61950469, 47461425, 15059448, 8291718, 17558356, 7937195, 15768925, 9047445, 6340712, 10774345, 10795597, 20809021, 48701865, 51091566, 41242615, 37208030, 42830626, 21296655, 61588900, 60772420, 56745534, 50065172, 62167253, 44186767, 167277977, 167412647, 61599553, 61793630, 17559280, 30840365, 6056719, 6023174, 14700148, 10699458, 7440434, 5830788, 16830531, 36374512, 12803565, 22055143, 27851830, 166882954, 43146673, 21868198, 44355835, 61079203, 49566268, 43390620, 48648504, 56494061, 41923576, 61835191, 63032743, 50389668, 43556762, 61952789, 10515859, 63411294, 61787527, 7691951, 21252862, 50058218, 61780119, 27880167, 61604840, 22236358, 61597374, 61579823, 45428002, 58926833, 63555859, 62326869, 39588863, 61605755, 40887919, 61597571, 61601524, 14167279, 24340641, 21966233, 21075844, 61580012, 61580937, 18214391, 9670834, 61573275, 8305836, 61669421, ...] nucleotidyltransferase activity
GO:0003677 -0.622 -4.303 0.000e+00 0.000e+00 369 155 [66926567, 68934118, 51907206, 56510025, 68645600, 46260937, 61571198, 61950469, 47461425, 15059448, 8291718, 17558356, 7937195, 15768925, 9047445, 6340712, 10774345, 10795597, 20809021, 48701865, 51091566, 41242615, 37208030, 42830626, 21296655, 61588900, 60772420, 56745534, 50065172, 62167253, 44186767, 167412647, 61599553, 17559280, 30840365, 6056719, 6023174, 14700148, 10699458, 7440434, 5830788, 16830531, 36374512, 12803565, 22055143, 27851830, 166882954, 43146673, 21868198, 61079203, 61952789, 7691951, 21252862, 50058218, 27880167, 61604840, 22236358, 61597374, 61579823, 45428002, 58926833, 63555859, 62326869, 39588863, 61605755, 40887919, 61597571, 61601524, 14167279, 24340641, 21966233, 21075844, 61580012, 61580937, 18214391, 9670834, 61573275, 8305836, 61669421, 61603176, 61601759, 7435501, 56735007, 65613889, 63632220, 58090628, 30077373, 26013941, 44284503, 66863306, 63185291, 41171397, 45190220, 21909748, 63027032, 62634255, 20706901, 62427434, 58137973, 62092597, ...] DNA binding
GO:0004634 -0.870 -3.487 0.000e+00 0.000e+00 43 19 [62743325, 62658191, 22213675, 18120033, 66797374, 62783504, 3624425, 20853105, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] phosphopyruvate hydratase activity
GO:0000287 -0.669 -3.414 0.000e+00 0.000e+00 113 42 [39279903, 62071220, 168126288, 41534199, 8102980, 53821637, 38613059, 62743325, 62143029, 42049385, 62198791, 8551124, 62658191, 62737033, 64587749, 63158778, 62853917, 63677227, 10822577, 54615426, 61965999, 21360480, 22213675, 18120033, 66797374, 62783504, 62289912, 65218941, 3624425, 20853105, 28234013, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] magnesium ion binding
GO:0016835 -0.770 -3.278 0.000e+00 0.000e+00 85 23 [62217311, 57701171, 62743325, 62658191, 20611399, 62207461, 22213675, 18120033, 66797374, 62783504, 3624425, 20853105, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] carbon-oxygen lyase activity
GO:0016781 -0.431 -3.183 0.000e+00 0.000e+00 302 218 [68757582, 48551975, 59573933, 36437635, 64455875, 66240602, 42784525, 36779731, 43056580, 58194975, 59590660, 67137330, 41650094, 66324771, 40653126, 47809732, 62986062, 66416823, 59382202, 61733256, 43640300, 21366390, 62740745, 61678241, 61701146, 167228497, 63000196, 61697822, 15392158, 16540060, 52628294, 62082610, 61678624, 39053068, 64622520, 51924715, 42863431, 50610839, 23335153, 50468391, 46980869, 43779205, 17629190, 36132573, 40213847, 61710750, 16841857, 56043654, 168096789, 7261272, 61715784, 66064320, 57076882, 3967585, 7554865, 18134283, 61719792, 6107407, 11790449, 5053713, 2271726, 2775482, 1963894, 39756635, 7609064, 10803750, 30295347, 49098505, 15165337, 61717374, 32808173, 11783818, 48309556, 5248047, 6028622, 8907106, 3545035, 12680181, 3710169, 10338470, 11005782, 61686338, 10511979, 62355720, 20874127, 21628356, 4077657, 8955380, 44507319, 166283021, 61723254, 7114893, 4228803, 61721447, 53043520, 6702801, 9050982, 33383509, 21125442, 20673079, ...] phosphotransferase activity, paired acceptors
GO:0016301 -0.385 -2.821 0.000e+00 0.000e+00 480 214 [21799656, 22349603, 62247377, 64925467, 20722321, 167526299, 62422222, 165866251, 52517748, 63185681, 43056580, 45593936, 40688875, 18128369, 47619855, 45919266, 62560655, 67137330, 166007049, 41650094, 40653126, 47809732, 62986062, 66416823, 59382202, 61733256, 43640300, 21366390, 38666650, 61678241, 61701146, 167228497, 61697822, 15392158, 16540060, 52628294, 62082610, 61678624, 39053068, 64622520, 51924715, 50610839, 23335153, 50468391, 62952131, 17629190, 40213847, 61710750, 16841857, 168096789, 7261272, 61715784, 3967585, 7554865, 18134283, 61719792, 6107407, 5053713, 2271726, 2775482, 1963894, 7609064, 10803750, 15165337, 61717374, 32808173, 5248047, 6028622, 8907106, 3545035, 12680181, 3710169, 10338470, 11005782, 61686338, 10511979, 62355720, 20874127, 21628356, 4077657, 8955380, 44507319, 166283021, 61723254, 7114893, 4228803, 61721447, 53043520, 6702801, 9050982, 33383509, 21125442, 20673079, 51148156, 61722089, 6343409, 8071617, 61731522, 61736645, 15304368, ...] kinase activity
GO:0016829 -0.486 -2.564 0.000e+00 1.394e-05 279 46 [15754209, 18137146, 168075980, 62217311, 37010279, 57701171, 65535760, 47787704, 166165052, 168061964, 63157973, 64182902, 63865771, 62743325, 65586747, 18213545, 63272810, 29774394, 63649356, 63517822, 62658191, 63973174, 20611399, 67497751, 49673151, 62207461, 61426290, 40859402, 44157917, 22213675, 18120033, 66797374, 62783504, 3624425, 20853105, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] lyase activity
GO:0004654 -0.702 -2.563 0.000e+00 1.255e-05 45 15 [61793630, 44355835, 49566268, 43390620, 48648504, 56494061, 41923576, 61835191, 63032743, 50389668, 43556762, 10515859, 63411294, 61787527, 61780119] polyribonucleotide nucleotidyltransferase activity
GO:0016874 -0.483 -2.403 0.000e+00 9.125e-05 245 39 [62359585, 31255317, 61964112, 62018486, 65135677, 17571629, 51305083, 62702496, 64709852, 67213458, 64164012, 165831755, 62468665, 66039359, 62517803, 167995278, 62840735, 61879238, 62492484, 54586926, 61930024, 10533506, 29053973, 30950615, 63858457, 61952129, 64502622, 52698315, 61904210, 61808732, 61840025, 61928230, 61891853, 61901890, 48778871, 51629989, 61714907, 166468321, 62120168] ligase activity
GO:0004518 -0.700 -2.297 0.000e+00 3.346e-04 30 11 [61793630, 49566268, 43390620, 41923576, 63032743, 43556762, 10515859, 63411294, 61787527, 61780119, 63401624] nuclease activity
GO:0016796 -0.700 -2.211 2.008e-04 7.721e-04 29 10 [61793630, 49566268, 43390620, 41923576, 63032743, 43556762, 10515859, 63411294, 61787527, 61780119] exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters
GO:0004540 -0.700 -2.210 4.058e-04 7.259e-04 29 10 [61793630, 49566268, 43390620, 41923576, 63032743, 43556762, 10515859, 63411294, 61787527, 61780119] ribonuclease activity
GO:0016879 -0.482 -2.139 4.186e-04 1.405e-03 114 26 [61964112, 62018486, 65135677, 17571629, 51305083, 64709852, 67213458, 64164012, 165831755, 62517803, 62840735, 61879238, 61930024, 10533506, 29053973, 30950615, 63858457, 61952129, 64502622, 52698315, 61904210, 61808732, 61840025, 61928230, 61891853, 61901890] ligase activity, forming carbon-nitrogen bonds
GO:0016614 -0.403 -1.993 2.161e-03 5.238e-03 150 37 [7011122, 166616289, 63505555, 63863560, 63958498, 10318713, 56135140, 61717636, 11307495, 166155431, 61686088, 10739365, 8550259, 51115316, 62274246, 38181119, 62737033, 40713606, 38860663, 61303090, 53916053, 64587749, 63158778, 11427336, 62853917, 168067151, 63677227, 10822577, 54615426, 61965999, 20822172, 21360480, 50196479, 38164996, 53819948, 61809381, 63464232] oxidoreductase activity, acting on CH-OH group of donors
GO:0003723 -0.380 -1.991 1.086e-03 5.011e-03 367 46 [165850968, 11332141, 62054342, 65259195, 44182220, 61893464, 66649599, 62018747, 166720030, 62017462, 42559031, 47520394, 65480581, 65242908, 45913613, 65518489, 6406070, 61793630, 44355835, 49566268, 43390620, 48648504, 56494061, 41923576, 61835191, 63032743, 50389668, 43556762, 10515859, 63411294, 61787527, 36091865, 67329767, 61780119, 67458415, 165823420, 166327905, 68568761, 44131449, 65477380, 70697066, 21053600, 67469358, 66838239, 56890477, 64167079] RNA binding
GO:0046872 -0.292 -1.899 6.787e-04 9.968e-03 488 112 [63098496, 38170520, 21834593, 6263025, 63079626, 62114668, 39279903, 4416015, 62515931, 10318713, 61599909, 65619550, 63230588, 62890909, 64549605, 61599853, 61601993, 22084793, 61717636, 166791155, 47787704, 62655429, 166165052, 63157973, 166155431, 62018747, 65999129, 62017462, 61686088, 62071220, 61986126, 61603708, 168126288, 41534199, 8102980, 53821637, 38613059, 168109762, 64182902, 63865771, 62743325, 61600015, 61963309, 62143029, 61600538, 42049385, 165714838, 166304100, 62198791, 64211477, 27694381, 65586747, 60255223, 41869870, 63007267, 64109059, 47654592, 37964574, 10739365, 50135248, 167530105, 49924705, 18213545, 62232545, 63272810, 8551124, 29774394, 63649356, 20607209, 61598699, 63517822, 62658191, 61588102, 63973174, 37345174, 64823101, 67497751, 46312448, 40859402, 62737033, 42863898, 64587749, 63158778, 62853917, 63677227, 10822577, 54615426, 61965999, 21360480, 10323127, 22213675, 18120033, 61809381, 66797374, 62783504, 62289912, 14653772, 65218941, 3624425, 20853105, ...] metal ion binding
GO:0016875 -0.581 -1.892 6.599e-03 9.932e-03 110 11 [62359585, 62702496, 62468665, 66039359, 62492484, 54586926, 48778871, 51629989, 61714907, 166468321, 62120168] ligase activity, forming carbon-oxygen bonds
GO:0051287 -0.443 -1.759 1.555e-02 2.502e-02 73 19 [63863560, 63958498, 56135140, 6997781, 11307495, 62943474, 63032818, 63371685, 62737033, 64587749, 63158778, 62853917, 63677227, 10822577, 54615426, 61965999, 21360480, 63600850, 61809381] NAD binding
GO:0016798 -0.416 -1.742 1.604e-02 2.689e-02 76 22 [13575738, 39013713, 167690499, 66536404, 53177315, 18978935, 65538005, 168124324, 62400701, 54157666, 41984885, 166027215, 166219312, 168249536, 61771909, 62035953, 167938999, 13569694, 167252077, 62146975, 13571215, 65262333] hydrolase activity, acting on glycosyl bonds
GO:0003735 -0.291 -1.603 1.828e-02 6.276e-02 360 55 [165850968, 11332141, 62054342, 67774188, 4009201, 65259195, 44182220, 167340047, 48590768, 167349682, 168017014, 29341916, 7259645, 67389484, 82054302, 166807349, 74406712, 67061811, 62018747, 166720030, 62017462, 20720618, 13581456, 66350717, 65886657, 66541818, 4774708, 66050469, 65480581, 65242908, 65518489, 6406070, 67641346, 66639541, 30291146, 33140401, 7354884, 36091865, 67329767, 67458415, 165823420, 166327905, 68568761, 44131449, 65477380, 66053289, 65977279, 68748656, 70697066, 21053600, 67469358, 66838239, 56890477, 67144272, 66453589] structural constituent of ribosome
GO:0070279 -0.306 -1.558 3.190e-02 7.741e-02 136 40 [27696183, 21808882, 168075980, 62743829, 61703706, 62783884, 63323004, 37010279, 167595271, 61748514, 165689798, 22197112, 61742431, 63286685, 62948337, 66510411, 49462236, 62718756, 61756955, 51344941, 30290988, 40544251, 66822118, 62207461, 37568190, 12023663, 65099450, 39202078, 56071476, 51146942, 62652073, 63013915, 61965999, 62284246, 52250379, 44274395, 63055945, 63086724, 9720195, 62875224] vitamin B6 binding
GO:0004553 -0.373 -1.539 4.999e-02 8.240e-02 75 21 [13575738, 39013713, 167690499, 66536404, 53177315, 18978935, 65538005, 168124324, 62400701, 54157666, 41984885, 166027215, 166219312, 168249536, 61771909, 62035953, 167938999, 13569694, 167252077, 62146975, 13571215] hydrolase activity, hydrolyzing O-glycosyl compounds

In [28]:
bp_rag


Out[28]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0040011 0.543 3.224 0.000e+00 0.000 274 85 [63837786, 165990924, 167953213, 168171488, 167966912, 13586931, 165936696, 62136808, 167570053, 64855697, 64780867, 62417891, 62405618, 62303301, 42831732, 62719918, 62849941, 168192733, 62771320, 62619244, 62923262, 62926584, 63144665, 28438217, 62002315, 165775316, 57751592, 63195134, 66593668, 63842059, 63275290, 64065097, 167641590, 13574239, 48437829, 52127537, 68252636, 167628538, 166007447, 167438835, 62565570, 62396394, 166874224, 167434350, 62085029, 13589494, 65988434, 64297496, 167832826, 167343151, 13586933, 167738934, 168200142, 66403957, 11407241, 44091081, 167337265, 11413856, 22310619, 167047560, 63798592, 10082333, 63500843, 63295556, 166530730, 67398658, 168112544, 28430116, 62300168, 11548874, 168001411, 166818826, 64573539, 63489079, 63911288, 63937175, 66399802, 64842974, 165887166, 166824805, 166695246, 62626786, 167344702, 167799665, 166636440] locomotion
GO:0006928 0.534 3.148 0.000e+00 0.000 270 81 [167953213, 168171488, 167966912, 13586931, 62136808, 167570053, 64855697, 64780867, 62417891, 62405618, 62303301, 42831732, 62719918, 62849941, 168192733, 62771320, 62619244, 62923262, 62926584, 63144665, 28438217, 62002315, 165775316, 57751592, 63195134, 66593668, 63842059, 63275290, 64065097, 167641590, 13574239, 48437829, 52127537, 68252636, 167628538, 166007447, 167438835, 62565570, 62396394, 166874224, 167434350, 62085029, 13589494, 65988434, 64297496, 167832826, 167343151, 13586933, 167738934, 168200142, 66403957, 11407241, 167337265, 11413856, 22310619, 167047560, 63798592, 10082333, 63500843, 63295556, 166530730, 67398658, 168112544, 28430116, 62300168, 11548874, 168001411, 166818826, 64573539, 63489079, 63911288, 63937175, 66399802, 64842974, 165887166, 166824805, 166695246, 62626786, 167344702, 167799665, 166636440] movement of cell or subcellular component
GO:0048870 0.534 3.142 0.000e+00 0.000 269 81 [167953213, 168171488, 167966912, 13586931, 62136808, 167570053, 64855697, 64780867, 62417891, 62405618, 62303301, 42831732, 62719918, 62849941, 168192733, 62771320, 62619244, 62923262, 62926584, 63144665, 28438217, 62002315, 165775316, 57751592, 63195134, 66593668, 63842059, 63275290, 64065097, 167641590, 13574239, 48437829, 52127537, 68252636, 167628538, 166007447, 167438835, 62565570, 62396394, 166874224, 167434350, 62085029, 13589494, 65988434, 64297496, 167832826, 167343151, 13586933, 167738934, 168200142, 66403957, 11407241, 167337265, 11413856, 22310619, 167047560, 63798592, 10082333, 63500843, 63295556, 166530730, 67398658, 168112544, 28430116, 62300168, 11548874, 168001411, 166818826, 64573539, 63489079, 63911288, 63937175, 66399802, 64842974, 165887166, 166824805, 166695246, 62626786, 167344702, 167799665, 166636440] cell motility
GO:0042558 0.648 2.104 5.870e-04 0.007 40 11 [31379006, 61964112, 62018486, 65135677, 63995561, 17571629, 51305083, 64709852, 67213458, 64164012, 165831755] pteridine-containing compound metabolic process
GO:0042559 0.640 2.002 2.145e-03 0.014 29 10 [61964112, 62018486, 65135677, 63995561, 17571629, 51305083, 64709852, 67213458, 64164012, 165831755] pteridine-containing compound biosynthetic process
GO:0006575 0.640 1.988 2.322e-03 0.013 30 10 [61964112, 62018486, 65135677, 63995561, 17571629, 51305083, 64709852, 67213458, 64164012, 165831755] cellular modified amino acid metabolic process
GO:1901605 0.438 1.807 8.340e-03 0.049 110 22 [63889213, 165956827, 63092817, 166239197, 27696183, 21808882, 63863560, 62743829, 166756527, 61703706, 65619550, 63323004, 37425343, 166114562, 20611399, 62207461, 22083024, 62840735, 62652073, 63437396, 63600850, 9720195] alpha-amino acid metabolic process
GO:0051234 0.328 1.796 3.290e-03 0.047 331 61 [167285315, 13587543, 167348034, 165992613, 167399046, 62160260, 21799059, 62047389, 62623865, 166635414, 49707019, 168124343, 11412988, 62344870, 28423332, 168161151, 63070669, 166208277, 28240379, 40674602, 62545344, 62072713, 21258712, 64530918, 165851092, 63132923, 65516796, 66978191, 31357673, 32955361, 40686252, 13203808, 32157942, 13841186, 6347838, 12378604, 8187004, 62946388, 6934942, 47513944, 37969849, 63199719, 10732421, 27603383, 62055617, 33383613, 62354250, 65627086, 63129880, 61865720, 63078357, 165706474, 61614285, 13570595, 167606365, 64582513, 165776049, 13568664, 4019294, 167556744, 65386242] establishment of localization
GO:0051179 0.328 1.795 3.550e-03 0.042 332 61 [167285315, 13587543, 167348034, 165992613, 167399046, 62160260, 21799059, 62047389, 62623865, 166635414, 49707019, 168124343, 11412988, 62344870, 28423332, 168161151, 63070669, 166208277, 28240379, 40674602, 62545344, 62072713, 21258712, 64530918, 165851092, 63132923, 65516796, 66978191, 31357673, 32955361, 40686252, 13203808, 32157942, 13841186, 6347838, 12378604, 8187004, 62946388, 6934942, 47513944, 37969849, 63199719, 10732421, 27603383, 62055617, 33383613, 62354250, 65627086, 63129880, 61865720, 63078357, 165706474, 61614285, 13570595, 167606365, 64582513, 165776049, 13568664, 4019294, 167556744, 65386242] localization
GO:0022900 0.518 1.784 1.424e-02 0.041 72 13 [62114668, 61599909, 61599853, 61601993, 61603708, 168109762, 61600015, 61600538, 37964574, 62232545, 20607209, 61598699, 61588102] electron transport chain
GO:0050794 0.459 1.729 1.845e-02 0.054 36 17 [63837786, 165873031, 165990924, 62304018, 167750483, 165936696, 66926567, 68934118, 165961991, 68645600, 68045078, 44091081, 61600015, 59827295, 66251821, 37727049, 65993244] regulation of cellular process
GO:0051188 0.489 1.728 2.132e-02 0.050 99 14 [15754209, 61964112, 62018486, 65135677, 63995561, 17571629, 51305083, 64709852, 67213458, 64164012, 42108500, 27694381, 165831755, 14665780] cofactor biosynthetic process
GO:0044042 0.510 1.710 2.181e-02 0.053 85 12 [18523127, 28436439, 40551040, 59156012, 63039326, 57028376, 65657046, 63112646, 38175368, 62718684, 27804972, 167277977] glucan metabolic process
GO:0005976 0.510 1.709 2.585e-02 0.049 86 12 [18523127, 28436439, 40551040, 59156012, 63039326, 57028376, 65657046, 63112646, 38175368, 62718684, 27804972, 167277977] polysaccharide metabolic process
GO:0000271 0.510 1.700 2.494e-02 0.049 80 12 [18523127, 28436439, 40551040, 59156012, 63039326, 57028376, 65657046, 63112646, 38175368, 62718684, 27804972, 167277977] polysaccharide biosynthetic process
GO:0005978 0.510 1.699 2.176e-02 0.046 69 12 [18523127, 28436439, 40551040, 59156012, 63039326, 57028376, 65657046, 63112646, 38175368, 62718684, 27804972, 167277977] glycogen biosynthetic process
GO:0006112 0.510 1.698 2.417e-02 0.043 74 12 [18523127, 28436439, 40551040, 59156012, 63039326, 57028376, 65657046, 63112646, 38175368, 62718684, 27804972, 167277977] energy reserve metabolic process
GO:0015980 0.510 1.695 2.101e-02 0.042 82 12 [18523127, 28436439, 40551040, 59156012, 63039326, 57028376, 65657046, 63112646, 38175368, 62718684, 27804972, 167277977] energy derivation by oxidation of organic compounds
GO:0009108 0.505 1.633 3.809e-02 0.060 77 11 [61964112, 62018486, 65135677, 63995561, 17571629, 51305083, 64709852, 67213458, 64164012, 165831755, 14665780] coenzyme biosynthetic process
GO:0044282 0.577 1.575 4.378e-02 0.080 35 7 [63092817, 166239197, 63505555, 61703706, 62445847, 64823101, 58900609] small molecule catabolic process

In [29]:
bp_wt


Out[29]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0032774 -0.653 -4.449 0.000e+00 0.000e+00 345 143 [61571198, 61950469, 47461425, 15059448, 8291718, 17558356, 7937195, 15768925, 9047445, 6340712, 10774345, 10795597, 20809021, 48701865, 51091566, 41242615, 37208030, 42830626, 21296655, 61588900, 60772420, 56745534, 50065172, 62167253, 44186767, 167412647, 61599553, 17559280, 30840365, 6056719, 6023174, 14700148, 10699458, 7440434, 5830788, 16830531, 36374512, 12803565, 22055143, 27851830, 166882954, 43146673, 21868198, 61079203, 61952789, 7691951, 21252862, 50058218, 27880167, 61604840, 22236358, 61597374, 61579823, 45428002, 58926833, 63555859, 62326869, 39588863, 61605755, 40887919, 61597571, 61601524, 14167279, 24340641, 21966233, 21075844, 61580012, 61580937, 18214391, 9670834, 61573275, 8305836, 61669421, 61603176, 61601759, 7435501, 56735007, 65613889, 63632220, 58090628, 30077373, 26013941, 44284503, 66863306, 63185291, 41171397, 45190220, 21909748, 63027032, 62634255, 20706901, 62427434, 58137973, 62092597, 59642867, 37935841, 62130826, 38315748, 58701908, 41204377, ...] RNA biosynthetic process
GO:0072350 -0.796 -3.228 0.000e+00 0.000e+00 29 20 [38181119, 62737033, 40713606, 38860663, 61303090, 53916053, 64587749, 63158778, 11427336, 62853917, 168067151, 63677227, 10822577, 54615426, 61965999, 20822172, 21360480, 50196479, 38164996, 53819948] tricarboxylic acid metabolic process
GO:0009259 -0.498 -2.877 0.000e+00 0.000e+00 414 66 [167029093, 167526299, 165866251, 62344870, 64711323, 63185681, 166165052, 63157973, 18134535, 64380885, 53022688, 40688875, 62072713, 20752463, 64530918, 69926951, 64182902, 63865771, 62743325, 62661009, 18128369, 47619855, 45919266, 32079045, 62560655, 166007049, 62354250, 54193303, 65627086, 18213545, 63272810, 8551124, 63649356, 38666650, 63517822, 62446788, 62658191, 63973174, 62636935, 22197670, 50712297, 65812454, 166287375, 22213675, 18120033, 66797374, 13568664, 62783504, 167057179, 64066327, 65218941, 3624425, 20853105, 28234013, 6131330, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] ribonucleotide metabolic process
GO:0009123 -0.498 -2.875 0.000e+00 0.000e+00 412 66 [167029093, 167526299, 165866251, 62344870, 64711323, 63185681, 166165052, 63157973, 18134535, 64380885, 53022688, 40688875, 62072713, 20752463, 64530918, 69926951, 64182902, 63865771, 62743325, 62661009, 18128369, 47619855, 45919266, 32079045, 62560655, 166007049, 62354250, 54193303, 65627086, 18213545, 63272810, 8551124, 63649356, 38666650, 63517822, 62446788, 62658191, 63973174, 62636935, 22197670, 50712297, 65812454, 166287375, 22213675, 18120033, 66797374, 13568664, 62783504, 167057179, 64066327, 65218941, 3624425, 20853105, 28234013, 6131330, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] nucleoside monophosphate metabolic process
GO:0019693 -0.486 -2.818 0.000e+00 0.000e+00 416 67 [167029093, 167526299, 63863560, 165866251, 62344870, 64711323, 63185681, 166165052, 63157973, 18134535, 64380885, 53022688, 40688875, 62072713, 20752463, 64530918, 69926951, 64182902, 63865771, 62743325, 62661009, 18128369, 47619855, 45919266, 32079045, 62560655, 166007049, 62354250, 54193303, 65627086, 18213545, 63272810, 8551124, 63649356, 38666650, 63517822, 62446788, 62658191, 63973174, 62636935, 22197670, 50712297, 65812454, 166287375, 22213675, 18120033, 66797374, 13568664, 62783504, 167057179, 64066327, 65218941, 3624425, 20853105, 28234013, 6131330, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] ribose phosphate metabolic process
GO:0009132 -0.498 -2.788 0.000e+00 0.000e+00 304 58 [167029093, 167526299, 165866251, 64711323, 63185681, 166165052, 63157973, 18134535, 64380885, 53022688, 40688875, 20752463, 69926951, 64182902, 63865771, 62743325, 62661009, 18128369, 47619855, 45919266, 32079045, 62560655, 166007049, 54193303, 18213545, 63272810, 8551124, 63649356, 38666650, 63517822, 62446788, 62658191, 63973174, 62636935, 22197670, 50712297, 65812454, 166287375, 22213675, 18120033, 66797374, 62783504, 65218941, 3624425, 20853105, 28234013, 6131330, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] nucleoside diphosphate metabolic process
GO:0046939 -0.498 -2.780 0.000e+00 0.000e+00 304 58 [167029093, 167526299, 165866251, 64711323, 63185681, 166165052, 63157973, 18134535, 64380885, 53022688, 40688875, 20752463, 69926951, 64182902, 63865771, 62743325, 62661009, 18128369, 47619855, 45919266, 32079045, 62560655, 166007049, 54193303, 18213545, 63272810, 8551124, 63649356, 38666650, 63517822, 62446788, 62658191, 63973174, 62636935, 22197670, 50712297, 65812454, 166287375, 22213675, 18120033, 66797374, 62783504, 65218941, 3624425, 20853105, 28234013, 6131330, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] nucleotide phosphorylation
GO:0009135 -0.498 -2.769 0.000e+00 0.000e+00 302 58 [167029093, 167526299, 165866251, 64711323, 63185681, 166165052, 63157973, 18134535, 64380885, 53022688, 40688875, 20752463, 69926951, 64182902, 63865771, 62743325, 62661009, 18128369, 47619855, 45919266, 32079045, 62560655, 166007049, 54193303, 18213545, 63272810, 8551124, 63649356, 38666650, 63517822, 62446788, 62658191, 63973174, 62636935, 22197670, 50712297, 65812454, 166287375, 22213675, 18120033, 66797374, 62783504, 65218941, 3624425, 20853105, 28234013, 6131330, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] purine nucleoside diphosphate metabolic process
GO:0046034 -0.478 -2.750 0.000e+00 0.000e+00 379 64 [167029093, 167526299, 165866251, 62344870, 64711323, 63185681, 166165052, 63157973, 18134535, 64380885, 53022688, 40688875, 62072713, 20752463, 64530918, 69926951, 64182902, 63865771, 62743325, 62661009, 18128369, 47619855, 45919266, 32079045, 62560655, 166007049, 62354250, 54193303, 65627086, 18213545, 63272810, 8551124, 63649356, 38666650, 63517822, 62446788, 62658191, 63973174, 62636935, 22197670, 50712297, 65812454, 166287375, 22213675, 18120033, 66797374, 13568664, 62783504, 65218941, 3624425, 20853105, 28234013, 6131330, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] ATP metabolic process
GO:0009141 -0.478 -2.745 0.000e+00 0.000e+00 381 64 [167029093, 167526299, 165866251, 62344870, 64711323, 63185681, 166165052, 63157973, 18134535, 64380885, 53022688, 40688875, 62072713, 20752463, 64530918, 69926951, 64182902, 63865771, 62743325, 62661009, 18128369, 47619855, 45919266, 32079045, 62560655, 166007049, 62354250, 54193303, 65627086, 18213545, 63272810, 8551124, 63649356, 38666650, 63517822, 62446788, 62658191, 63973174, 62636935, 22197670, 50712297, 65812454, 166287375, 22213675, 18120033, 66797374, 13568664, 62783504, 65218941, 3624425, 20853105, 28234013, 6131330, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] nucleoside triphosphate metabolic process
GO:0009126 -0.478 -2.739 0.000e+00 0.000e+00 409 64 [167029093, 167526299, 165866251, 62344870, 64711323, 63185681, 166165052, 63157973, 18134535, 64380885, 53022688, 40688875, 62072713, 20752463, 64530918, 69926951, 64182902, 63865771, 62743325, 62661009, 18128369, 47619855, 45919266, 32079045, 62560655, 166007049, 62354250, 54193303, 65627086, 18213545, 63272810, 8551124, 63649356, 38666650, 63517822, 62446788, 62658191, 63973174, 62636935, 22197670, 50712297, 65812454, 166287375, 22213675, 18120033, 66797374, 13568664, 62783504, 65218941, 3624425, 20853105, 28234013, 6131330, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] purine nucleoside monophosphate metabolic process
GO:0072524 -0.485 -2.734 0.000e+00 0.000e+00 305 59 [167029093, 167526299, 63863560, 165866251, 64711323, 63185681, 166165052, 63157973, 18134535, 64380885, 53022688, 40688875, 20752463, 69926951, 64182902, 63865771, 62743325, 62661009, 18128369, 47619855, 45919266, 32079045, 62560655, 166007049, 54193303, 18213545, 63272810, 8551124, 63649356, 38666650, 63517822, 62446788, 62658191, 63973174, 62636935, 22197670, 50712297, 65812454, 166287375, 22213675, 18120033, 66797374, 62783504, 65218941, 3624425, 20853105, 28234013, 6131330, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] pyridine-containing compound metabolic process
GO:0009150 -0.478 -2.729 0.000e+00 0.000e+00 412 64 [167029093, 167526299, 165866251, 62344870, 64711323, 63185681, 166165052, 63157973, 18134535, 64380885, 53022688, 40688875, 62072713, 20752463, 64530918, 69926951, 64182902, 63865771, 62743325, 62661009, 18128369, 47619855, 45919266, 32079045, 62560655, 166007049, 62354250, 54193303, 65627086, 18213545, 63272810, 8551124, 63649356, 38666650, 63517822, 62446788, 62658191, 63973174, 62636935, 22197670, 50712297, 65812454, 166287375, 22213675, 18120033, 66797374, 13568664, 62783504, 65218941, 3624425, 20853105, 28234013, 6131330, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] purine ribonucleotide metabolic process
GO:0006733 -0.485 -2.720 0.000e+00 0.000e+00 305 59 [167029093, 167526299, 63863560, 165866251, 64711323, 63185681, 166165052, 63157973, 18134535, 64380885, 53022688, 40688875, 20752463, 69926951, 64182902, 63865771, 62743325, 62661009, 18128369, 47619855, 45919266, 32079045, 62560655, 166007049, 54193303, 18213545, 63272810, 8551124, 63649356, 38666650, 63517822, 62446788, 62658191, 63973174, 62636935, 22197670, 50712297, 65812454, 166287375, 22213675, 18120033, 66797374, 62783504, 65218941, 3624425, 20853105, 28234013, 6131330, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] oxidoreduction coenzyme metabolic process
GO:1901135 -0.458 -2.705 0.000e+00 0.000e+00 447 74 [62247377, 167029093, 167526299, 63863560, 62422222, 165866251, 52517748, 62344870, 64711323, 63185681, 166165052, 63157973, 18134535, 62018747, 64380885, 62017462, 53022688, 40688875, 62072713, 20752463, 64530918, 69926951, 64182902, 63865771, 62743325, 62661009, 18128369, 47619855, 45919266, 32079045, 62560655, 166007049, 62354250, 54193303, 65627086, 18213545, 63272810, 8551124, 63649356, 38666650, 63517822, 62446788, 62658191, 63973174, 62636935, 22197670, 50712297, 65812454, 166287375, 22213675, 18120033, 13586908, 66797374, 13568664, 62783504, 11404724, 167057179, 64066327, 65218941, 3624425, 20853105, 28234013, 6131330, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] carbohydrate derivative metabolic process
GO:0044724 -0.465 -2.630 0.000e+00 0.000e+00 336 62 [167029093, 63505555, 167526299, 165866251, 64711323, 63185681, 166165052, 63157973, 18134535, 64380885, 53022688, 40688875, 20752463, 69926951, 64182902, 63865771, 62743325, 62661009, 18128369, 47619855, 45919266, 32079045, 62560655, 166007049, 54193303, 18213545, 63272810, 8551124, 63649356, 38666650, 63517822, 62446788, 62658191, 63973174, 62445847, 64823101, 62636935, 22197670, 50712297, 65812454, 166287375, 58900609, 22213675, 18120033, 66797374, 62783504, 65218941, 3624425, 20853105, 28234013, 6131330, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] single-organism carbohydrate catabolic process
GO:0044265 -0.702 -2.602 0.000e+00 0.000e+00 48 15 [61793630, 44355835, 49566268, 43390620, 48648504, 56494061, 41923576, 61835191, 63032743, 50389668, 43556762, 10515859, 63411294, 61787527, 61780119] cellular macromolecule catabolic process
GO:0009057 -0.702 -2.600 0.000e+00 0.000e+00 56 15 [61793630, 44355835, 49566268, 43390620, 48648504, 56494061, 41923576, 61835191, 63032743, 50389668, 43556762, 10515859, 63411294, 61787527, 61780119] macromolecule catabolic process
GO:0019439 -0.702 -2.583 0.000e+00 0.000e+00 54 15 [61793630, 44355835, 49566268, 43390620, 48648504, 56494061, 41923576, 61835191, 63032743, 50389668, 43556762, 10515859, 63411294, 61787527, 61780119] aromatic compound catabolic process
GO:0048519 -0.702 -2.580 0.000e+00 0.000e+00 46 15 [61793630, 44355835, 49566268, 43390620, 48648504, 56494061, 41923576, 61835191, 63032743, 50389668, 43556762, 10515859, 63411294, 61787527, 61780119] negative regulation of biological process
GO:0016052 -0.452 -2.578 0.000e+00 0.000e+00 339 63 [167690499, 167029093, 63505555, 167526299, 165866251, 64711323, 63185681, 166165052, 63157973, 18134535, 64380885, 53022688, 40688875, 20752463, 69926951, 64182902, 63865771, 62743325, 62661009, 18128369, 47619855, 45919266, 32079045, 62560655, 166007049, 54193303, 18213545, 63272810, 8551124, 63649356, 38666650, 63517822, 62446788, 62658191, 63973174, 62445847, 64823101, 62636935, 22197670, 50712297, 65812454, 166287375, 58900609, 22213675, 18120033, 66797374, 62783504, 65218941, 3624425, 20853105, 28234013, 6131330, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] carbohydrate catabolic process
GO:0016071 -0.702 -2.571 0.000e+00 0.000e+00 45 15 [61793630, 44355835, 49566268, 43390620, 48648504, 56494061, 41923576, 61835191, 63032743, 50389668, 43556762, 10515859, 63411294, 61787527, 61780119] mRNA metabolic process
GO:0009117 -0.432 -2.567 0.000e+00 0.000e+00 496 74 [167029093, 167526299, 63863560, 52065887, 165866251, 62515931, 66618270, 62344870, 64711323, 67469592, 63185681, 166165052, 63157973, 18134535, 64380885, 53022688, 40688875, 62072713, 20752463, 64530918, 69926951, 64182902, 63865771, 62743325, 62661009, 18128369, 47619855, 63006542, 45919266, 32079045, 62560655, 166007049, 62354250, 54193303, 65627086, 18213545, 63272810, 8551124, 63649356, 38666650, 63517822, 62446788, 62658191, 63973174, 62636935, 22197670, 50712297, 65812454, 62274246, 166287375, 62517803, 22213675, 18120033, 66797374, 13568664, 62783504, 167057179, 64066327, 65218941, 3624425, 20853105, 28234013, 6131330, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] nucleotide metabolic process
GO:0006753 -0.432 -2.551 0.000e+00 5.025e-06 497 74 [167029093, 167526299, 63863560, 52065887, 165866251, 62515931, 66618270, 62344870, 64711323, 67469592, 63185681, 166165052, 63157973, 18134535, 64380885, 53022688, 40688875, 62072713, 20752463, 64530918, 69926951, 64182902, 63865771, 62743325, 62661009, 18128369, 47619855, 63006542, 45919266, 32079045, 62560655, 166007049, 62354250, 54193303, 65627086, 18213545, 63272810, 8551124, 63649356, 38666650, 63517822, 62446788, 62658191, 63973174, 62636935, 22197670, 50712297, 65812454, 62274246, 166287375, 62517803, 22213675, 18120033, 66797374, 13568664, 62783504, 167057179, 64066327, 65218941, 3624425, 20853105, 28234013, 6131330, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] nucleoside phosphate metabolic process
GO:0072521 -0.431 -2.529 0.000e+00 4.824e-06 475 70 [167029093, 167526299, 52065887, 165866251, 66618270, 62344870, 64711323, 67469592, 63185681, 166165052, 63157973, 18134535, 64380885, 53022688, 40688875, 62072713, 20752463, 64530918, 69926951, 64182902, 63865771, 62743325, 62661009, 18128369, 47619855, 63006542, 45919266, 32079045, 62560655, 166007049, 62354250, 54193303, 65627086, 18213545, 63272810, 8551124, 63649356, 38666650, 63517822, 62446788, 62658191, 63973174, 62636935, 22197670, 50712297, 65812454, 62274246, 166287375, 62517803, 22213675, 18120033, 66797374, 13568664, 62783504, 65218941, 3624425, 20853105, 28234013, 6131330, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] purine-containing compound metabolic process
GO:0044712 -0.430 -2.467 0.000e+00 2.319e-05 355 65 [63092817, 166239197, 167029093, 63505555, 167526299, 165866251, 61703706, 64711323, 63185681, 166165052, 63157973, 18134535, 64380885, 53022688, 40688875, 20752463, 69926951, 64182902, 63865771, 62743325, 62661009, 18128369, 47619855, 45919266, 32079045, 62560655, 166007049, 54193303, 18213545, 63272810, 8551124, 63649356, 38666650, 63517822, 62446788, 62658191, 63973174, 62445847, 64823101, 62636935, 22197670, 50712297, 65812454, 166287375, 58900609, 22213675, 18120033, 66797374, 62783504, 65218941, 3624425, 20853105, 28234013, 6131330, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] single-organism catabolic process
GO:1901361 -0.617 -2.319 2.037e-04 1.117e-04 55 16 [62515931, 61793630, 44355835, 49566268, 43390620, 48648504, 56494061, 41923576, 61835191, 63032743, 50389668, 43556762, 10515859, 63411294, 61787527, 61780119] organic cyclic compound catabolic process
GO:0044270 -0.617 -2.301 2.101e-04 1.551e-04 55 16 [62515931, 61793630, 44355835, 49566268, 43390620, 48648504, 56494061, 41923576, 61835191, 63032743, 50389668, 43556762, 10515859, 63411294, 61787527, 61780119] cellular nitrogen compound catabolic process
GO:0006732 -0.381 -2.281 0.000e+00 1.955e-04 391 76 [62579418, 167029093, 167526299, 63863560, 165866251, 64711323, 61901179, 61964112, 62018486, 65135677, 61880488, 63185681, 63603065, 63995561, 17571629, 51305083, 166165052, 63849179, 64709852, 63157973, 67213458, 18134535, 64380885, 64164012, 53022688, 40688875, 20752463, 69926951, 64182902, 63865771, 62743325, 63900260, 62661009, 18128369, 47619855, 45919266, 32079045, 62560655, 166007049, 54193303, 18213545, 63272810, 8551124, 165831755, 63649356, 38666650, 63517822, 62446788, 62658191, 63973174, 62636935, 22197670, 50712297, 65812454, 166287375, 22213675, 18120033, 14665780, 66797374, 62783504, 65218941, 3624425, 20853105, 28234013, 6131330, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] coenzyme metabolic process
GO:0019222 -0.540 -2.270 2.064e-04 2.050e-04 59 22 [66926567, 68934118, 68645600, 61793630, 44355835, 49566268, 43390620, 48648504, 56494061, 41923576, 61835191, 63032743, 50389668, 43556762, 10515859, 63411294, 61787527, 61780119, 59827295, 66251821, 37727049, 65993244] regulation of metabolic process
GO:0006396 -0.700 -2.220 0.000e+00 3.346e-04 32 10 [61793630, 49566268, 43390620, 41923576, 63032743, 43556762, 10515859, 63411294, 61787527, 61780119] RNA processing
GO:0060255 -0.529 -2.191 4.153e-04 4.523e-04 58 21 [66926567, 68934118, 68645600, 61793630, 44355835, 49566268, 43390620, 48648504, 56494061, 41923576, 61835191, 63032743, 50389668, 43556762, 10515859, 63411294, 61787527, 61780119, 66251821, 37727049, 65993244] regulation of macromolecule metabolic process
GO:0051186 -0.363 -2.184 0.000e+00 4.715e-04 413 79 [62579418, 15754209, 167029093, 167526299, 63863560, 165866251, 64711323, 61901179, 61964112, 62018486, 65135677, 61880488, 63185681, 63603065, 63995561, 17571629, 51305083, 166165052, 63849179, 64709852, 63157973, 67213458, 18134535, 64380885, 64164012, 53022688, 40688875, 42108500, 20752463, 69926951, 64182902, 63865771, 62743325, 63900260, 62661009, 18128369, 47619855, 45919266, 32079045, 62560655, 27694381, 166007049, 54193303, 18213545, 63272810, 8551124, 165831755, 63649356, 38666650, 63517822, 62446788, 62658191, 63973174, 62636935, 22197670, 50712297, 65812454, 166287375, 22213675, 18120033, 14665780, 66797374, 62783504, 65218941, 3624425, 20853105, 28234013, 6131330, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] cofactor metabolic process
GO:0010468 -0.529 -2.175 0.000e+00 4.966e-04 57 21 [66926567, 68934118, 68645600, 61793630, 44355835, 49566268, 43390620, 48648504, 56494061, 41923576, 61835191, 63032743, 50389668, 43556762, 10515859, 63411294, 61787527, 61780119, 66251821, 37727049, 65993244] regulation of gene expression
GO:0006091 -0.333 -2.071 0.000e+00 1.447e-03 474 91 [62114668, 18523127, 167029093, 167526299, 165866251, 28436439, 61599909, 64711323, 64549605, 61599853, 61601993, 63185681, 40551040, 59156012, 63039326, 57028376, 166165052, 65657046, 63112646, 63157973, 18134535, 64380885, 53022688, 40688875, 61603708, 20752463, 69926951, 168109762, 64182902, 63865771, 38175368, 62743325, 62661009, 61600015, 18128369, 47619855, 61963309, 62718684, 45919266, 61600538, 32079045, 166304100, 62560655, 64211477, 166007049, 60255223, 64109059, 27804972, 37964574, 50135248, 54193303, 49924705, 18213545, 62232545, 63272810, 8551124, 63649356, 20607209, 61598699, 38666650, 63517822, 62446788, 62658191, 61588102, 63973174, 62636935, 22197670, 50712297, 167277977, 65812454, 166287375, 22213675, 18120033, 66797374, 62783504, 65218941, 3624425, 20853105, 28234013, 6131330, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] generation of precursor metabolites and energy
GO:0009056 -0.332 -2.029 0.000e+00 2.037e-03 409 82 [167690499, 63092817, 166239197, 167029093, 63505555, 167526299, 165866251, 61703706, 62515931, 64711323, 63185681, 166165052, 63157973, 18134535, 64380885, 53022688, 40688875, 20752463, 69926951, 64182902, 63865771, 62743325, 62661009, 18128369, 47619855, 45919266, 32079045, 62560655, 166007049, 54193303, 18213545, 63272810, 8551124, 63649356, 38666650, 63517822, 62446788, 62658191, 63973174, 62445847, 64823101, 62636935, 22197670, 50712297, 65812454, 61793630, 166287375, 44355835, 49566268, 43390620, 48648504, 56494061, 41923576, 61835191, 63032743, 50389668, 43556762, 10515859, 63411294, 58900609, 61787527, 61780119, 22213675, 18120033, 66797374, 62783504, 65218941, 3624425, 20853105, 28234013, 6131330, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] catabolic process
GO:0043038 -0.581 -1.902 5.510e-03 6.148e-03 110 11 [62359585, 62702496, 62468665, 66039359, 62492484, 54586926, 48778871, 51629989, 61714907, 166468321, 62120168] amino acid activation
GO:0034660 -0.581 -1.879 6.748e-03 7.205e-03 112 11 [62359585, 62702496, 62468665, 66039359, 62492484, 54586926, 48778871, 51629989, 61714907, 166468321, 62120168] ncRNA metabolic process
GO:0019538 -0.313 -1.853 1.763e-03 8.551e-03 478 72 [165850968, 11332141, 168124483, 62054342, 67774188, 4416015, 66831306, 4009201, 65259195, 44182220, 167340047, 48590768, 167349682, 168017014, 29341916, 7259645, 67389484, 82054302, 166807349, 74406712, 67061811, 62018747, 166720030, 62017462, 20720618, 13581456, 66350717, 65886657, 66541818, 4774708, 66050469, 36306027, 62943474, 62228244, 62403068, 62543620, 51091566, 65480581, 65242908, 65518489, 6406070, 67641346, 66639541, 30291146, 33140401, 7354884, 36091865, 67329767, 50058218, 67458415, 165823420, 166327905, 68568761, 44131449, 65477380, 13570862, 165780748, 51277953, 66053289, 65977279, 48778871, 51629989, 68748656, 50491176, 70697066, 21053600, 67469358, 66838239, 56890477, 62120168, 67144272, 66453589] protein metabolic process
GO:0006412 -0.327 -1.829 5.030e-03 9.887e-03 372 58 [165850968, 11332141, 62054342, 67774188, 4009201, 65259195, 44182220, 167340047, 48590768, 167349682, 168017014, 29341916, 7259645, 67389484, 82054302, 166807349, 74406712, 67061811, 62018747, 166720030, 62017462, 20720618, 13581456, 66350717, 65886657, 66541818, 4774708, 66050469, 65480581, 65242908, 65518489, 6406070, 67641346, 66639541, 30291146, 33140401, 7354884, 36091865, 67329767, 67458415, 165823420, 166327905, 68568761, 44131449, 65477380, 66053289, 65977279, 48778871, 51629989, 68748656, 70697066, 21053600, 67469358, 66838239, 56890477, 62120168, 67144272, 66453589] translation
GO:0043043 -0.321 -1.804 3.822e-03 1.161e-02 377 59 [165850968, 11332141, 62054342, 67774188, 4009201, 65259195, 44182220, 167340047, 48590768, 167349682, 168017014, 29341916, 7259645, 67389484, 82054302, 166807349, 74406712, 67061811, 62018747, 166720030, 62017462, 20720618, 13581456, 66350717, 42108500, 65886657, 66541818, 4774708, 66050469, 65480581, 65242908, 65518489, 6406070, 67641346, 66639541, 30291146, 33140401, 7354884, 36091865, 67329767, 67458415, 165823420, 166327905, 68568761, 44131449, 65477380, 66053289, 65977279, 48778871, 51629989, 68748656, 70697066, 21053600, 67469358, 66838239, 56890477, 62120168, 67144272, 66453589] peptide biosynthetic process
GO:0006518 -0.321 -1.795 4.583e-03 1.221e-02 378 59 [165850968, 11332141, 62054342, 67774188, 4009201, 65259195, 44182220, 167340047, 48590768, 167349682, 168017014, 29341916, 7259645, 67389484, 82054302, 166807349, 74406712, 67061811, 62018747, 166720030, 62017462, 20720618, 13581456, 66350717, 42108500, 65886657, 66541818, 4774708, 66050469, 65480581, 65242908, 65518489, 6406070, 67641346, 66639541, 30291146, 33140401, 7354884, 36091865, 67329767, 67458415, 165823420, 166327905, 68568761, 44131449, 65477380, 66053289, 65977279, 48778871, 51629989, 68748656, 70697066, 21053600, 67469358, 66838239, 56890477, 62120168, 67144272, 66453589] peptide metabolic process
GO:0044267 -0.308 -1.737 4.969e-03 1.824e-02 413 61 [165850968, 11332141, 62054342, 67774188, 66831306, 4009201, 65259195, 44182220, 167340047, 48590768, 167349682, 168017014, 29341916, 7259645, 67389484, 82054302, 166807349, 74406712, 67061811, 62018747, 166720030, 62017462, 20720618, 13581456, 66350717, 65886657, 66541818, 4774708, 66050469, 36306027, 62228244, 65480581, 65242908, 65518489, 6406070, 67641346, 66639541, 30291146, 33140401, 7354884, 36091865, 67329767, 67458415, 165823420, 166327905, 68568761, 44131449, 65477380, 66053289, 65977279, 48778871, 51629989, 68748656, 70697066, 21053600, 67469358, 66838239, 56890477, 62120168, 67144272, 66453589] cellular protein metabolic process
GO:1901137 -0.617 -1.602 3.913e-02 4.176e-02 102 6 [62344870, 62354250, 65627086, 13568664, 167057179, 64066327] carbohydrate derivative biosynthetic process
GO:0009124 -0.617 -1.594 4.298e-02 4.268e-02 98 6 [62344870, 62354250, 65627086, 13568664, 167057179, 64066327] nucleoside monophosphate biosynthetic process
GO:0046390 -0.617 -1.594 3.748e-02 4.184e-02 100 6 [62344870, 62354250, 65627086, 13568664, 167057179, 64066327] ribose phosphate biosynthetic process
GO:0043604 -0.257 -1.506 3.093e-02 6.583e-02 411 69 [165850968, 11332141, 62054342, 67774188, 4009201, 65259195, 61964112, 44182220, 62018486, 65135677, 63995561, 17571629, 51305083, 64709852, 67213458, 167340047, 48590768, 167349682, 168017014, 29341916, 7259645, 67389484, 82054302, 166807349, 74406712, 67061811, 62018747, 166720030, 62017462, 20720618, 64164012, 13581456, 66350717, 42108500, 65886657, 66541818, 4774708, 66050469, 165831755, 65480581, 65242908, 65518489, 6406070, 67641346, 66639541, 30291146, 33140401, 7354884, 36091865, 67329767, 67458415, 165823420, 166327905, 68568761, 44131449, 65477380, 66053289, 65977279, 48778871, 51629989, 68748656, 70697066, 21053600, 67469358, 66838239, 56890477, 62120168, 67144272, 66453589] amide biosynthetic process
GO:0043603 -0.248 -1.455 4.302e-02 8.471e-02 414 70 [165850968, 11332141, 62054342, 67774188, 4009201, 62515931, 65259195, 61964112, 44182220, 62018486, 65135677, 63995561, 17571629, 51305083, 64709852, 67213458, 167340047, 48590768, 167349682, 168017014, 29341916, 7259645, 67389484, 82054302, 166807349, 74406712, 67061811, 62018747, 166720030, 62017462, 20720618, 64164012, 13581456, 66350717, 42108500, 65886657, 66541818, 4774708, 66050469, 165831755, 65480581, 65242908, 65518489, 6406070, 67641346, 66639541, 30291146, 33140401, 7354884, 36091865, 67329767, 67458415, 165823420, 166327905, 68568761, 44131449, 65477380, 66053289, 65977279, 48778871, 51629989, 68748656, 70697066, 21053600, 67469358, 66838239, 56890477, 62120168, 67144272, 66453589] cellular amide metabolic process

In [30]:
cc_rag


Out[30]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0042995 0.534 3.138 0.000e+00 0.000e+00 269 81 [167953213, 168171488, 167966912, 13586931, 62136808, 167570053, 64855697, 64780867, 62417891, 62405618, 62303301, 42831732, 62719918, 62849941, 168192733, 62771320, 62619244, 62923262, 62926584, 63144665, 28438217, 62002315, 165775316, 57751592, 63195134, 66593668, 63842059, 63275290, 64065097, 167641590, 13574239, 48437829, 52127537, 68252636, 167628538, 166007447, 167438835, 62565570, 62396394, 166874224, 167434350, 62085029, 13589494, 65988434, 64297496, 167832826, 167343151, 13586933, 167738934, 168200142, 66403957, 11407241, 167337265, 11413856, 22310619, 167047560, 63798592, 10082333, 63500843, 63295556, 166530730, 67398658, 168112544, 28430116, 62300168, 11548874, 168001411, 166818826, 64573539, 63489079, 63911288, 63937175, 66399802, 64842974, 165887166, 166824805, 166695246, 62626786, 167344702, 167799665, 166636440] cell projection
GO:0044463 0.529 2.985 0.000e+00 0.000e+00 229 66 [167953213, 168171488, 167966912, 13586931, 62136808, 167570053, 64855697, 64780867, 62417891, 62405618, 62303301, 42831732, 62719918, 62849941, 168192733, 62771320, 62619244, 62923262, 62926584, 63144665, 28438217, 62002315, 13574239, 167628538, 167438835, 166874224, 167434350, 62085029, 13589494, 65988434, 64297496, 167832826, 167343151, 13586933, 167738934, 168200142, 66403957, 11407241, 167337265, 11413856, 22310619, 167047560, 63798592, 10082333, 63500843, 63295556, 166530730, 67398658, 168112544, 28430116, 62300168, 11548874, 168001411, 166818826, 64573539, 63489079, 63911288, 63937175, 66399802, 64842974, 165887166, 166824805, 166695246, 62626786, 167344702, 167799665] cell projection part
GO:0044422 0.492 2.964 0.000e+00 0.000e+00 402 90 [167953213, 168171488, 167966912, 13586931, 62136808, 167570053, 64855697, 64780867, 62417891, 62405618, 62303301, 42831732, 62719918, 62849941, 168192733, 62771320, 62619244, 62923262, 62926584, 63144665, 28438217, 62002315, 13574239, 167628538, 65259195, 167438835, 166874224, 167434350, 62085029, 13589494, 44182220, 65988434, 64297496, 167832826, 167343151, 13586933, 167738934, 168200142, 167340047, 48590768, 168017014, 29341916, 7259645, 67389484, 82054302, 166807349, 74406712, 67061811, 66403957, 166720030, 20720618, 11407241, 167337265, 66350717, 11413856, 22310619, 167047560, 65886657, 66541818, 4774708, 63798592, 10082333, 66050469, 63500843, 63295556, 166530730, 67398658, 168112544, 28430116, 62300168, 11548874, 168001411, 166818826, 64573539, 63489079, 63911288, 63937175, 66399802, 64842974, 165887166, 166824805, 166695246, 62626786, 167344702, 167799665, 65480581, 65242908, 65518489, 6406070, 65477380] organelle part
GO:0044459 0.531 2.390 0.000e+00 2.728e-05 119 29 [168161151, 28240379, 40674602, 62545344, 21258712, 63132923, 65516796, 66978191, 31357673, 32955361, 40686252, 13203808, 32157942, 13841186, 6347838, 12378604, 8187004, 62946388, 6934942, 47513944, 37969849, 63199719, 10732421, 27603383, 62055617, 33383613, 63129880, 61865720, 63078357] plasma membrane part
GO:1990351 0.531 2.387 0.000e+00 2.182e-05 117 29 [168161151, 28240379, 40674602, 62545344, 21258712, 63132923, 65516796, 66978191, 31357673, 32955361, 40686252, 13203808, 32157942, 13841186, 6347838, 12378604, 8187004, 62946388, 6934942, 47513944, 37969849, 63199719, 10732421, 27603383, 62055617, 33383613, 63129880, 61865720, 63078357] transporter complex
GO:1904949 0.531 2.386 0.000e+00 1.819e-05 117 29 [168161151, 28240379, 40674602, 62545344, 21258712, 63132923, 65516796, 66978191, 31357673, 32955361, 40686252, 13203808, 32157942, 13841186, 6347838, 12378604, 8187004, 62946388, 6934942, 47513944, 37969849, 63199719, 10732421, 27603383, 62055617, 33383613, 63129880, 61865720, 63078357] ATPase complex
GO:0098797 0.531 2.386 0.000e+00 1.559e-05 117 29 [168161151, 28240379, 40674602, 62545344, 21258712, 63132923, 65516796, 66978191, 31357673, 32955361, 40686252, 13203808, 32157942, 13841186, 6347838, 12378604, 8187004, 62946388, 6934942, 47513944, 37969849, 63199719, 10732421, 27603383, 62055617, 33383613, 63129880, 61865720, 63078357] plasma membrane protein complex
GO:0043190 0.531 2.381 0.000e+00 1.364e-05 115 29 [168161151, 28240379, 40674602, 62545344, 21258712, 63132923, 65516796, 66978191, 31357673, 32955361, 40686252, 13203808, 32157942, 13841186, 6347838, 12378604, 8187004, 62946388, 6934942, 47513944, 37969849, 63199719, 10732421, 27603383, 62055617, 33383613, 63129880, 61865720, 63078357] ATP-binding cassette (ABC) transporter complex
GO:0098796 0.460 2.183 0.000e+00 3.395e-04 171 35 [62344870, 168161151, 28240379, 40674602, 62545344, 62072713, 21258712, 165851092, 63132923, 65516796, 66978191, 31357673, 32955361, 40686252, 13203808, 32157942, 13841186, 6347838, 12378604, 8187004, 62946388, 6934942, 47513944, 37969849, 63199719, 10732421, 27603383, 62055617, 33383613, 62354250, 65627086, 63129880, 61865720, 63078357, 13568664] membrane protein complex
GO:0043234 0.460 2.171 1.883e-04 3.383e-04 180 35 [62344870, 168161151, 28240379, 40674602, 62545344, 62072713, 21258712, 165851092, 63132923, 65516796, 66978191, 31357673, 32955361, 40686252, 13203808, 32157942, 13841186, 6347838, 12378604, 8187004, 62946388, 6934942, 47513944, 37969849, 63199719, 10732421, 27603383, 62055617, 33383613, 62354250, 65627086, 63129880, 61865720, 63078357, 13568664] protein complex
GO:0015935 0.526 2.063 2.295e-03 9.820e-04 96 19 [65259195, 167340047, 48590768, 168017014, 29341916, 7259645, 67389484, 82054302, 166807349, 74406712, 67061811, 166720030, 20720618, 66350717, 65886657, 66541818, 4774708, 66050469, 65477380] small ribosomal subunit
GO:0044425 0.356 1.724 9.871e-03 1.535e-02 191 37 [62344870, 168161151, 28240379, 40674602, 62545344, 62072713, 21258712, 165851092, 63132923, 65516796, 66978191, 31357673, 32955361, 40686252, 13203808, 32157942, 13841186, 6347838, 12378604, 8187004, 62946388, 6934942, 47513944, 37969849, 63199719, 10732421, 27603383, 62055617, 33383613, 62354250, 65627086, 63129880, 61865720, 63078357, 165706474, 13568664, 167150261] membrane part
GO:0044391 0.401 1.696 2.221e-02 1.671e-02 159 24 [65259195, 44182220, 167340047, 48590768, 168017014, 29341916, 7259645, 67389484, 82054302, 166807349, 74406712, 67061811, 166720030, 20720618, 66350717, 65886657, 66541818, 4774708, 66050469, 65480581, 65242908, 65518489, 6406070, 65477380] ribosomal subunit
GO:0044446 0.401 1.693 2.090e-02 1.589e-02 169 24 [65259195, 44182220, 167340047, 48590768, 168017014, 29341916, 7259645, 67389484, 82054302, 166807349, 74406712, 67061811, 166720030, 20720618, 66350717, 65886657, 66541818, 4774708, 66050469, 65480581, 65242908, 65518489, 6406070, 65477380] intracellular organelle part

In [31]:
cc_wt


Out[31]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0000015 -0.870 -3.496 0.000e+00 0.000e+00 43 19 [62743325, 62658191, 22213675, 18120033, 66797374, 62783504, 3624425, 20853105, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] phosphopyruvate hydratase complex
GO:0044445 -0.870 -3.453 0.000e+00 0.000e+00 47 19 [62743325, 62658191, 22213675, 18120033, 66797374, 62783504, 3624425, 20853105, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174] cytosolic part
GO:1902494 -0.490 -2.699 0.000e+00 0.000e+00 202 56 [7522635, 22519241, 63652778, 168124324, 168161151, 28240379, 40674602, 62545344, 43045244, 21258712, 65221038, 62743325, 63132923, 65516796, 66978191, 31357673, 32955361, 40686252, 13203808, 32157942, 13841186, 6347838, 12378604, 8187004, 62946388, 6934942, 47513944, 37969849, 63199719, 10732421, 27603383, 62055617, 33383613, 63129880, 61865720, 63078357, 62658191, 63401624, 22213675, 18120033, 66797374, 62783504, 3624425, 20853105, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 13571215, 17549174] catalytic complex
GO:0044444 -0.430 -2.607 0.000e+00 0.000e+00 422 80 [165850968, 11332141, 62054342, 67774188, 4009201, 7522635, 65259195, 22519241, 63652778, 44182220, 167340047, 48590768, 167349682, 168017014, 29341916, 7259645, 67389484, 82054302, 166807349, 74406712, 67061811, 62018747, 166720030, 62017462, 20720618, 13581456, 66350717, 43045244, 65221038, 65886657, 62743325, 66541818, 4774708, 66050469, 62658191, 65480581, 65242908, 65518489, 6406070, 67641346, 66639541, 30291146, 33140401, 7354884, 36091865, 67329767, 67458415, 165823420, 166327905, 68568761, 44131449, 65477380, 22213675, 18120033, 61809381, 66053289, 66797374, 62783504, 65977279, 68748656, 70697066, 21053600, 67469358, 66838239, 56890477, 3624425, 20853105, 10876818, 45981629, 46324053, 62809084, 21126143, 5189919, 20745054, 66137094, 31709972, 62848403, 17549174, 67144272, 66453589] cytoplasmic part
GO:0005737 -0.471 -2.194 4.234e-04 4.848e-04 264 31 [63092817, 166239197, 61703706, 62359585, 62702496, 18950035, 54139955, 36306027, 8550259, 62228244, 62468665, 62405280, 62299040, 165706474, 66039359, 1488186, 62492484, 54586926, 64117322, 13567160, 63600850, 48778871, 51629989, 167057179, 64066327, 61714907, 166468321, 62120168, 167938999, 13569694, 63464232] cytoplasm
GO:0043229 -0.340 -1.842 6.066e-03 9.561e-03 327 51 [165850968, 11332141, 62054342, 67774188, 4009201, 44182220, 167340047, 48590768, 167349682, 168017014, 29341916, 7259645, 67389484, 82054302, 166807349, 74406712, 67061811, 62018747, 166720030, 62017462, 20720618, 13581456, 66350717, 65886657, 66541818, 4774708, 66050469, 67641346, 66639541, 30291146, 33140401, 7354884, 36091865, 67329767, 67458415, 165823420, 166327905, 68568761, 44131449, 65477380, 66053289, 65977279, 68748656, 70697066, 21053600, 67469358, 61950988, 66838239, 56890477, 67144272, 66453589] intracellular organelle
GO:0043232 -0.340 -1.838 3.035e-03 8.311e-03 320 51 [165850968, 11332141, 62054342, 67774188, 4009201, 44182220, 167340047, 48590768, 167349682, 168017014, 29341916, 7259645, 67389484, 82054302, 166807349, 74406712, 67061811, 62018747, 166720030, 62017462, 20720618, 13581456, 66350717, 65886657, 66541818, 4774708, 66050469, 67641346, 66639541, 30291146, 33140401, 7354884, 36091865, 67329767, 67458415, 165823420, 166327905, 68568761, 44131449, 65477380, 66053289, 65977279, 68748656, 70697066, 21053600, 67469358, 61950988, 66838239, 56890477, 67144272, 66453589] intracellular non-membrane-bounded organelle
GO:0005840 -0.328 -1.759 7.912e-03 1.312e-02 319 50 [165850968, 11332141, 62054342, 67774188, 4009201, 44182220, 167340047, 48590768, 167349682, 168017014, 29341916, 7259645, 67389484, 82054302, 166807349, 74406712, 67061811, 62018747, 166720030, 62017462, 20720618, 13581456, 66350717, 65886657, 66541818, 4774708, 66050469, 67641346, 66639541, 30291146, 33140401, 7354884, 36091865, 67329767, 67458415, 165823420, 166327905, 68568761, 44131449, 65477380, 66053289, 65977279, 68748656, 70697066, 21053600, 67469358, 66838239, 56890477, 67144272, 66453589] ribosome
GO:1990904 -0.291 -1.596 1.878e-02 3.439e-02 360 55 [165850968, 11332141, 62054342, 67774188, 4009201, 65259195, 44182220, 167340047, 48590768, 167349682, 168017014, 29341916, 7259645, 67389484, 82054302, 166807349, 74406712, 67061811, 62018747, 166720030, 62017462, 20720618, 13581456, 66350717, 65886657, 66541818, 4774708, 66050469, 65480581, 65242908, 65518489, 6406070, 67641346, 66639541, 30291146, 33140401, 7354884, 36091865, 67329767, 67458415, 165823420, 166327905, 68568761, 44131449, 65477380, 66053289, 65977279, 68748656, 70697066, 21053600, 67469358, 66838239, 56890477, 67144272, 66453589] ribonucleoprotein complex

RT vs WT Human/Mouse


In [32]:
out_dir = "RT_WT_hm_gsea"
df = pd.read_csv(os.path.join(BASE,"RT_WT_deseq_results.csv"))
df = df[(df.padj.abs()<=0.2)]
df = df[df.human_mouse]
df['log2FoldChange'] = -1 * df['log2FoldChange']
rank_df = df[['Unnamed: 0', 'log2FoldChange']].rename(columns={'Unnamed: 0': 'gene_name', 'log2FoldChange': 'rank'})
rank_df = rank_df.sort_values('rank').reset_index(drop=True)
mf_res = run_go_gsea(rank_df, mf_map_f, seed=1111, outdir=out_dir)
bp_res = run_go_gsea(rank_df, bp_map_f, seed=1111, outdir=out_dir)
mf_rt = mf_res.query('nes > 0 and pval < 0.05').sort_values('nes', ascending=False)
mf_wt = mf_res.query('nes < 0 and pval < 0.05').sort_values('nes', ascending=True)
bp_rt = bp_res.query('nes > 0 and pval < 0.05').sort_values('nes', ascending=False)
bp_wt = bp_res.query('nes < 0 and pval < 0.05').sort_values('nes', ascending=True)


2017-04-04 12:45:23,893 Parsing data files for GSEA.............................
/usr/lib/python3/dist-packages/numpy/lib/arraysetops.py:379: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
  mask |= (ar1 == a)
2017-04-04 12:45:23,945 0007 gene_sets used for further statistical testing.....
2017-04-04 12:45:23,945 Start to run GSEA...Might take a while..................
2017-04-04 12:45:24,847 Start to generate gseapy reports, and produce figures...
/usr/lib/python3/dist-packages/matplotlib/figure.py:1744: UserWarning: This figure includes Axes that are not compatible with tight_layout, so its results might be incorrect.
  warnings.warn("This figure includes Axes that are not "
2017-04-04 12:45:26,811 Congratulations...GSEAPY run successfully...............
2017-04-04 12:45:26,830 Parsing data files for GSEA.............................
2017-04-04 12:45:26,889 0010 gene_sets used for further statistical testing.....
2017-04-04 12:45:26,890 Start to run GSEA...Might take a while..................
2017-04-04 12:45:28,165 Start to generate gseapy reports, and produce figures...
2017-04-04 12:45:31,028 Congratulations...GSEAPY run successfully...............

In [33]:
mf_rt


Out[33]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0030246 0.577 1.538 0.044 0.193 31 7 [165643482, 165647385, 61499891, 165653125, 165647386, 165643378, 165643381] carbohydrate binding

In [34]:
mf_wt


Out[34]:
es nes pval fdr gene_set_size matched_size genes name
Term

In [35]:
bp_rt


Out[35]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0065007 0.649 1.997 8.066e-04 0.012 86 11 [165648111, 165648112, 61499238, 61499613, 61503068, 165636196, 165642139, 165646068, 165661488, 61457133, 165661076] biological regulation
GO:0050789 0.663 1.845 6.288e-03 0.021 80 8 [165648111, 165648112, 61499238, 61503068, 165636196, 165642139, 165646068, 61457133] regulation of biological process

In [36]:
bp_wt


Out[36]:
es nes pval fdr gene_set_size matched_size genes name
Term

RT vs WT Non-Human/Mouse


In [37]:
out_dir = "RT_WT_gsea"
df = pd.read_csv(os.path.join(BASE,"RT_WT_deseq_results.csv"))
df = df[(df.padj.abs()<=0.2)]
df = df[~df.human_mouse]
df['log2FoldChange'] = -1 * df['log2FoldChange']
rank_df = df[['Unnamed: 0', 'log2FoldChange']].rename(columns={'Unnamed: 0': 'gene_name', 'log2FoldChange': 'rank'})
rank_df = rank_df.sort_values('rank').reset_index(drop=True)

In [38]:
mf_res = run_go_gsea(rank_df, mf_map_f, seed=1111, outdir=out_dir)
bp_res = run_go_gsea(rank_df, bp_map_f, seed=1111, outdir=out_dir)
cc_res = run_go_gsea(rank_df, cc_map_f, seed=1111, outdir=out_dir)
mf_rt = mf_res.query('nes > 0 and pval < 0.05').sort_values('nes', ascending=False)
mf_wt = mf_res.query('nes < 0 and pval < 0.05').sort_values('nes', ascending=True)
bp_rt = bp_res.query('nes > 0 and pval < 0.05').sort_values('nes', ascending=False)
bp_wt = bp_res.query('nes < 0 and pval < 0.05').sort_values('nes', ascending=True)
cc_rt = cc_res.query('nes > 0 and pval < 0.05').sort_values('nes', ascending=False)
cc_wt = cc_res.query('nes < 0 and pval < 0.05').sort_values('nes', ascending=True)


2017-04-04 12:45:31,283 Parsing data files for GSEA.............................
/usr/lib/python3/dist-packages/numpy/lib/arraysetops.py:379: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
  mask |= (ar1 == a)
2017-04-04 12:45:31,548 0076 gene_sets used for further statistical testing.....
2017-04-04 12:45:31,549 Start to run GSEA...Might take a while..................
2017-04-04 12:46:44,974 Start to generate gseapy reports, and produce figures...
/usr/lib/python3/dist-packages/matplotlib/figure.py:1744: UserWarning: This figure includes Axes that are not compatible with tight_layout, so its results might be incorrect.
  warnings.warn("This figure includes Axes that are not "
2017-04-04 12:46:50,503 Congratulations...GSEAPY run successfully...............
2017-04-04 12:46:50,528 Parsing data files for GSEA.............................
2017-04-04 12:46:50,810 0093 gene_sets used for further statistical testing.....
2017-04-04 12:46:50,811 Start to run GSEA...Might take a while..................
2017-04-04 12:48:22,983 Start to generate gseapy reports, and produce figures...
2017-04-04 12:48:28,604 Congratulations...GSEAPY run successfully...............
2017-04-04 12:48:28,610 Parsing data files for GSEA.............................
2017-04-04 12:48:28,665 0021 gene_sets used for further statistical testing.....
2017-04-04 12:48:28,666 Start to run GSEA...Might take a while..................
2017-04-04 12:48:50,390 Start to generate gseapy reports, and produce figures...
2017-04-04 12:48:55,940 Congratulations...GSEAPY run successfully...............

In [39]:
mf_rt


Out[39]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0004618 0.625 2.605 0.000e+00 1.942e-04 78 21 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4559493, 4737261, 45207415, 33420375, 22187812, 67028544, 59725586, 54913980, 4220178, 18128369, 65935692, 168089107, 66846572, 62829929, 63123662] phosphoglycerate kinase activity
GO:0016774 0.570 2.481 0.000e+00 1.457e-04 111 24 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4559493, 4737261, 45207415, 33420375, 22187812, 67028544, 59725586, 54913980, 3884277, 4220178, 18128369, 63123377, 65935692, 168089107, 66846572, 62829929, 13604374, 63123662] phosphotransferase activity, carboxyl group as acceptor
GO:0003723 0.339 2.072 1.527e-04 1.489e-02 367 79 [7655641, 64669875, 20323736, 33709212, 5730052, 10185112, 8974409, 5141220, 17035162, 8283720, 52960359, 65259195, 26879329, 23226729, 6962424, 15891127, 29630113, 23720124, 8107184, 20132923, 11332141, 165850968, 16968363, 40487328, 38183434, 5365520, 15916898, 61892960, 3492858, 4100571, 62054342, 41621220, 62224782, 10593880, 36697039, 61884939, 38302786, 23721515, 33208200, 30459755, 12493950, 31342205, 12690700, 10631876, 5753625, 30556349, 61893464, 44182220, 68927583, 4582849, 59885854, 167619418, 64742627, 65657914, 62896518, 65777235, 62322368, 9904239, 21252244, 36091865, 67329767, 65477380, 67968100, 37858962, 33732979, 66744947, 20822927, 67292411, 61756207, 166327905, 165823420, 67458415, 65669111, 70697066, 21053600, 66838239, 56890477, 29262834, 64167079] RNA binding
GO:0022892 0.545 2.058 1.214e-03 1.275e-02 89 16 [3885199, 1994037, 29978920, 33721585, 38210955, 54503535, 21357752, 32363526, 1809293, 268176, 21432496, 12867643, 27807827, 63810043, 64582513, 165706474] substrate-specific transporter activity
GO:0022857 0.476 1.959 4.743e-03 2.366e-02 212 20 [3885199, 1994037, 29978920, 33721585, 38210955, 54503535, 21357752, 32363526, 1809293, 268176, 21432496, 12867643, 47513944, 37969849, 63374013, 27807827, 28273397, 63810043, 64582513, 165706474] transmembrane transporter activity
GO:0001882 0.356 1.873 4.115e-03 3.969e-02 398 44 [5888442, 80382425, 5730052, 10185112, 8974409, 21138590, 12661961, 32794085, 26879329, 40640683, 69205977, 12999155, 23375966, 6243639, 4100571, 61982117, 36454371, 61884939, 49556056, 61106614, 5753625, 30556349, 16579503, 61893464, 69572327, 15782696, 80394470, 67719393, 15769577, 168124362, 167619418, 38421939, 66146108, 62727257, 10288858, 13297453, 37822499, 20642101, 43782565, 51285943, 15295447, 165685554, 29262834, 3557492] nucleoside binding
GO:0016301 0.327 1.845 2.740e-03 4.271e-02 480 57 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4559493, 4737261, 45207415, 21799656, 33420375, 62247377, 167526299, 17583418, 22187812, 61635847, 67028544, 59725586, 54913980, 3884277, 52517748, 62422222, 63185681, 13585577, 52152229, 66492431, 63266944, 61708790, 4220178, 18128369, 61733256, 67137330, 47809732, 66416823, 59382202, 62986062, 40653126, 42129940, 62942343, 36117032, 51371961, 48698283, 62102911, 63123377, 65935692, 168089107, 62109485, 66846572, 51336959, 64346968, 55261886, 48298182, 62829929, 59827295, 13604374, 63123662, 62098267] kinase activity
GO:0016614 0.366 1.781 1.184e-02 5.954e-02 150 34 [10318713, 13684061, 6155443, 7011122, 11147909, 166616289, 16967630, 63958498, 56134344, 26904631, 27290903, 29001612, 16965587, 29983272, 20853009, 7496609, 27407984, 63505555, 12905190, 8550259, 62329349, 62298783, 20839749, 51213068, 51313098, 62853917, 63332989, 167277486, 63235820, 51115316, 63662802, 63648739, 63464232, 61809381] oxidoreductase activity, acting on CH-OH group of donors
GO:0003735 0.272 1.748 3.471e-03 6.653e-02 360 95 [7655641, 64669875, 20323736, 33709212, 19107849, 29630217, 5141220, 17035162, 8283720, 60453073, 5645650, 65259195, 28829095, 165941560, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 11332141, 165850968, 16968363, 40487328, 38183434, 5365520, 15916898, 3492858, 62054342, 41621220, 62224782, 23449836, 10593880, 36697039, 38302786, 23721515, 33208200, 30459755, 12493950, 31342205, 12690700, 44182220, 3576806, 68927583, 4582849, 59885854, 64742627, 65657914, 69613400, 38731273, 67911420, 39007615, 66583625, 65777235, 66782633, 9904239, 21252244, 65506212, 65977068, 167623679, 64474525, 42272589, 36091865, 66752541, 67329767, 65477380, 167990362, 65626218, 67968100, 67247141, 37858962, 33732979, 66744947, 20822927, 38249992, 67292411, 66053289, 13581456, 67383571, 166327905, 165823420, 67458415, 68373997, 10276368, 65669111, 70697066, 21053600, 66838239, 56890477, 33140401, 166036375] structural constituent of ribosome
GO:0019001 0.321 1.659 2.244e-02 1.074e-01 248 41 [5888442, 80382425, 5730052, 10185112, 8974409, 21138590, 12661961, 32794085, 26879329, 40640683, 69205977, 4100571, 61982117, 36454371, 61884939, 49556056, 61106614, 5753625, 30556349, 16579503, 61893464, 69572327, 15782696, 80394470, 67719393, 15769577, 168124362, 167619418, 38421939, 66146108, 62727257, 10288858, 13297453, 37822499, 20642101, 43782565, 51285943, 15295447, 165685554, 29262834, 3557492] guanyl nucleotide binding
GO:0001883 0.321 1.652 1.801e-02 1.027e-01 248 41 [5888442, 80382425, 5730052, 10185112, 8974409, 21138590, 12661961, 32794085, 26879329, 40640683, 69205977, 4100571, 61982117, 36454371, 61884939, 49556056, 61106614, 5753625, 30556349, 16579503, 61893464, 69572327, 15782696, 80394470, 67719393, 15769577, 168124362, 167619418, 38421939, 66146108, 62727257, 10288858, 13297453, 37822499, 20642101, 43782565, 51285943, 15295447, 165685554, 29262834, 3557492] purine nucleoside binding
GO:0016831 0.506 1.615 3.886e-02 1.176e-01 88 10 [21276719, 51212653, 55408710, 48323766, 61982117, 36454371, 61106614, 15754209, 45349478, 22196793] carboxy-lyase activity
GO:0016820 0.523 1.606 4.395e-02 1.152e-01 190 9 [1994037, 32363526, 1809293, 268176, 12867643, 47513944, 37969849, 63374013, 28273397] hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances
GO:0042623 0.605 1.581 4.084e-02 1.234e-01 68 6 [1994037, 32363526, 1809293, 268176, 12867643, 61950988] ATPase activity, coupled
GO:0070279 0.343 1.547 4.962e-02 1.404e-01 136 27 [61703706, 21276719, 51212653, 55408710, 48323766, 63323004, 37010279, 65415020, 37828207, 10968755, 55061408, 168130513, 62783884, 27696183, 49072591, 21808882, 166738288, 62956953, 165689798, 22197112, 61742431, 21812180, 62718756, 46701851, 62284246, 63013915, 62875224] vitamin B6 binding

In [40]:
mf_wt


Out[40]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0004634 -0.577 -2.335 0.000e+00 0.005 43 16 [29629717, 23089117, 17564385, 17549174, 20853105, 62848403, 31709972, 62566960, 3624425, 20745054, 46324053, 45981629, 5189919, 10876818, 21126143, 62809084] phosphopyruvate hydratase activity
GO:0016798 -0.427 -2.163 2.532e-04 0.014 76 30 [11310495, 11409356, 13575738, 11310502, 167568891, 8550179, 53177315, 66536404, 18978935, 167683569, 62488243, 62035953, 63376055, 63922748, 168249536, 167639021, 61777171, 62521472, 36284522, 167252077, 61761442, 166205751, 51133511, 61941182, 167549118, 62146975, 13605039, 13571215, 62450924, 65262333] hydrolase activity, acting on glycosyl bonds
GO:0016835 -0.468 -2.115 1.449e-03 0.014 85 21 [29629717, 23089117, 80889105, 17564385, 62217311, 20611399, 17549174, 20853105, 62848403, 31709972, 62566960, 21791871, 51262100, 3624425, 20745054, 46324053, 45981629, 5189919, 10876818, 21126143, 62809084] carbon-oxygen lyase activity
GO:0030246 -0.575 -2.084 1.827e-03 0.013 31 12 [18135548, 11310502, 61777171, 20895349, 63655654, 61768284, 36284522, 61721575, 51133511, 13571510, 167549118, 13571215] carbohydrate binding
GO:0004553 -0.409 -2.055 1.979e-03 0.013 75 29 [11310495, 11409356, 13575738, 11310502, 167568891, 8550179, 53177315, 66536404, 18978935, 167683569, 62488243, 62035953, 63376055, 63922748, 168249536, 167639021, 61777171, 62521472, 36284522, 167252077, 61761442, 166205751, 51133511, 61941182, 167549118, 62146975, 13605039, 13571215, 62450924] hydrolase activity, hydrolyzing O-glycosyl compounds
GO:0000287 -0.279 -1.534 4.113e-02 0.303 113 39 [29629717, 9654148, 23089117, 25933508, 17589318, 26904631, 27290903, 29001612, 29983272, 20853009, 7496609, 28314259, 22516735, 8551124, 17564385, 62071220, 17549174, 20853105, 62853917, 60553857, 62848403, 31709972, 62176760, 63235820, 63662802, 63648739, 62566960, 61756207, 13574916, 65218941, 3624425, 28234013, 20745054, 46324053, 45981629, 5189919, 10876818, 21126143, 62809084] magnesium ion binding
GO:0046872 -0.214 -1.499 3.099e-02 0.307 488 87 [4715355, 29629717, 10318713, 9654148, 23089117, 6998407, 25933508, 7618450, 167451486, 63441836, 17589318, 4416015, 50252877, 166487064, 26904631, 27290903, 29001612, 29983272, 20853009, 7496609, 62515931, 28314259, 27407984, 62114668, 22516735, 64427981, 42827541, 64182902, 8551124, 17564385, 36356543, 64211477, 39493763, 47787704, 65323654, 66198980, 66019350, 65700587, 64424621, 36510691, 62071220, 22197507, 62073848, 168109762, 64823101, 17549174, 20853105, 62853917, 60553857, 51141976, 166574781, 62848403, 31709972, 62176760, 54721784, 63235820, 167849528, 63662802, 63648739, 22606442, 62960491, 10323127, 167278898, 62566960, 61756207, 13574916, 41253846, 167279252, 14653772, 65218941, 62216988, 65690420, 65762645, 166491001, 64479173, 3624425, 28234013, 61809381, 20745054, 46324053, 45981629, 5189919, 10876818, 21126143, 62809084, 61608244, 166278783] metal ion binding

In [41]:
bp_rt


Out[41]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0040011 0.362 2.061 6.275e-04 0.058 274 57 [168171488, 167307068, 13580518, 13586931, 167570053, 62303301, 42831732, 64855697, 64780867, 62417891, 62405618, 62136808, 62719918, 62849941, 57751592, 52127537, 13574239, 48437829, 68252636, 62771320, 63144665, 167641590, 62619244, 62923262, 62926584, 166007447, 28438217, 63195134, 63275290, 63842059, 64065097, 66593668, 62002315, 167738934, 66403957, 62565570, 62396394, 11407241, 167337265, 167047560, 13589494, 165880634, 167438835, 67398658, 63489079, 166530730, 168112544, 166818826, 64573539, 168001411, 63911288, 63937175, 168185530, 168106741, 168173199, 166250719, 166636440] locomotion
GO:0048870 0.362 2.046 0.000e+00 0.034 269 57 [168171488, 167307068, 13580518, 13586931, 167570053, 62303301, 42831732, 64855697, 64780867, 62417891, 62405618, 62136808, 62719918, 62849941, 57751592, 52127537, 13574239, 48437829, 68252636, 62771320, 63144665, 167641590, 62619244, 62923262, 62926584, 166007447, 28438217, 63195134, 63275290, 63842059, 64065097, 66593668, 62002315, 167738934, 66403957, 62565570, 62396394, 11407241, 167337265, 167047560, 13589494, 165880634, 167438835, 67398658, 63489079, 166530730, 168112544, 166818826, 64573539, 168001411, 63911288, 63937175, 168185530, 168106741, 168173199, 166250719, 166636440] cell motility
GO:0006928 0.362 2.043 9.539e-04 0.023 270 57 [168171488, 167307068, 13580518, 13586931, 167570053, 62303301, 42831732, 64855697, 64780867, 62417891, 62405618, 62136808, 62719918, 62849941, 57751592, 52127537, 13574239, 48437829, 68252636, 62771320, 63144665, 167641590, 62619244, 62923262, 62926584, 166007447, 28438217, 63195134, 63275290, 63842059, 64065097, 66593668, 62002315, 167738934, 66403957, 62565570, 62396394, 11407241, 167337265, 167047560, 13589494, 165880634, 167438835, 67398658, 63489079, 166530730, 168112544, 166818826, 64573539, 168001411, 63911288, 63937175, 168185530, 168106741, 168173199, 166250719, 166636440] movement of cell or subcellular component
GO:0072350 0.599 1.836 1.027e-02 0.100 29 9 [13684061, 78477008, 80889105, 26904631, 29983272, 20853009, 7496609, 3740901, 62853917] tricarboxylic acid metabolic process
GO:0044267 0.280 1.817 3.021e-03 0.093 413 101 [7655641, 64669875, 20323736, 33709212, 27212193, 38310093, 19107849, 29630217, 5141220, 17035162, 8283720, 60453073, 5645650, 65259195, 28829095, 165941560, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 11332141, 165850968, 16968363, 40487328, 38183434, 5365520, 15916898, 3492858, 62054342, 41621220, 62224782, 23449836, 10593880, 36697039, 38302786, 23721515, 33208200, 30459755, 12493950, 31342205, 12690700, 21157792, 44182220, 3576806, 68927583, 4582849, 59885854, 64742627, 65657914, 28150928, 69613400, 38731273, 67911420, 39007615, 66583625, 65777235, 66782633, 66339926, 9904239, 21252244, 65506212, 65977068, 167623679, 64474525, 42272589, 167278898, 36091865, 66752541, 67329767, 65477380, 167990362, 65626218, 67968100, 67247141, 37858962, 33732979, 66744947, 20822927, 38249992, 67292411, 66053289, 13581456, 67383571, 166327905, 165823420, 67458415, 68373997, 10276368, 65669111, 70697066, 21053600, 66838239, 56890477, 33140401, ...] cellular protein metabolic process
GO:1902578 0.457 1.815 8.095e-03 0.078 132 18 [3885199, 1994037, 29978920, 33721585, 38210955, 54503535, 21357752, 32363526, 1809293, 268176, 21432496, 29629513, 12867643, 27807827, 63810043, 64582513, 165706474, 67703402] single-organism localization
GO:0006412 0.269 1.737 6.115e-03 0.118 372 96 [7655641, 64669875, 20323736, 33709212, 19107849, 29630217, 5141220, 17035162, 8283720, 60453073, 5645650, 65259195, 28829095, 165941560, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 11332141, 165850968, 16968363, 40487328, 38183434, 5365520, 15916898, 3492858, 62054342, 41621220, 62224782, 23449836, 10593880, 36697039, 38302786, 23721515, 33208200, 30459755, 12493950, 31342205, 12690700, 44182220, 3576806, 68927583, 4582849, 59885854, 64742627, 65657914, 69613400, 38731273, 67911420, 39007615, 66583625, 65777235, 66782633, 66339926, 9904239, 21252244, 65506212, 65977068, 167623679, 64474525, 42272589, 36091865, 66752541, 67329767, 65477380, 167990362, 65626218, 67968100, 67247141, 37858962, 33732979, 66744947, 20822927, 38249992, 67292411, 66053289, 13581456, 67383571, 166327905, 165823420, 67458415, 68373997, 10276368, 65669111, 70697066, 21053600, 66838239, 56890477, 33140401, 166036375] translation
GO:0043043 0.269 1.733 6.947e-03 0.106 377 96 [7655641, 64669875, 20323736, 33709212, 19107849, 29630217, 5141220, 17035162, 8283720, 60453073, 5645650, 65259195, 28829095, 165941560, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 11332141, 165850968, 16968363, 40487328, 38183434, 5365520, 15916898, 3492858, 62054342, 41621220, 62224782, 23449836, 10593880, 36697039, 38302786, 23721515, 33208200, 30459755, 12493950, 31342205, 12690700, 44182220, 3576806, 68927583, 4582849, 59885854, 64742627, 65657914, 69613400, 38731273, 67911420, 39007615, 66583625, 65777235, 66782633, 66339926, 9904239, 21252244, 65506212, 65977068, 167623679, 64474525, 42272589, 36091865, 66752541, 67329767, 65477380, 167990362, 65626218, 67968100, 67247141, 37858962, 33732979, 66744947, 20822927, 38249992, 67292411, 66053289, 13581456, 67383571, 166327905, 165823420, 67458415, 68373997, 10276368, 65669111, 70697066, 21053600, 66838239, 56890477, 33140401, 166036375] peptide biosynthetic process
GO:0006518 0.269 1.732 5.055e-03 0.095 378 96 [7655641, 64669875, 20323736, 33709212, 19107849, 29630217, 5141220, 17035162, 8283720, 60453073, 5645650, 65259195, 28829095, 165941560, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 11332141, 165850968, 16968363, 40487328, 38183434, 5365520, 15916898, 3492858, 62054342, 41621220, 62224782, 23449836, 10593880, 36697039, 38302786, 23721515, 33208200, 30459755, 12493950, 31342205, 12690700, 44182220, 3576806, 68927583, 4582849, 59885854, 64742627, 65657914, 69613400, 38731273, 67911420, 39007615, 66583625, 65777235, 66782633, 66339926, 9904239, 21252244, 65506212, 65977068, 167623679, 64474525, 42272589, 36091865, 66752541, 67329767, 65477380, 167990362, 65626218, 67968100, 67247141, 37858962, 33732979, 66744947, 20822927, 38249992, 67292411, 66053289, 13581456, 67383571, 166327905, 165823420, 67458415, 68373997, 10276368, 65669111, 70697066, 21053600, 66838239, 56890477, 33140401, 166036375] peptide metabolic process
GO:0009127 0.652 1.721 2.018e-02 0.092 95 6 [1994037, 32363526, 1809293, 268176, 12867643, 63180877] purine nucleoside monophosphate biosynthetic process
GO:0043604 0.265 1.715 7.055e-03 0.087 411 98 [7655641, 64669875, 20323736, 33709212, 19107849, 29630217, 5141220, 17035162, 8283720, 60453073, 5645650, 65259195, 28829095, 165941560, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 11332141, 165850968, 16968363, 40487328, 38183434, 5365520, 15916898, 3492858, 62054342, 41621220, 62224782, 23449836, 10593880, 36697039, 38302786, 23721515, 33208200, 30459755, 12493950, 31342205, 12690700, 44182220, 3576806, 68927583, 4582849, 59885854, 17571629, 63995561, 64742627, 65657914, 69613400, 38731273, 67911420, 39007615, 66583625, 65777235, 66782633, 66339926, 9904239, 21252244, 65506212, 65977068, 167623679, 64474525, 42272589, 36091865, 66752541, 67329767, 65477380, 167990362, 65626218, 67968100, 67247141, 37858962, 33732979, 66744947, 20822927, 38249992, 67292411, 66053289, 13581456, 67383571, 166327905, 165823420, 67458415, 68373997, 10276368, 65669111, 70697066, 21053600, 66838239, 56890477, 33140401, 166036375] amide biosynthetic process
GO:0043603 0.264 1.711 7.148e-03 0.082 414 99 [7655641, 64669875, 20323736, 33709212, 19107849, 29630217, 5141220, 17035162, 8283720, 60453073, 5645650, 65259195, 28829095, 165941560, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 11332141, 165850968, 16968363, 40487328, 38183434, 5365520, 15916898, 3492858, 62054342, 62515931, 41621220, 62224782, 23449836, 10593880, 36697039, 38302786, 23721515, 33208200, 30459755, 12493950, 31342205, 12690700, 44182220, 3576806, 68927583, 4582849, 59885854, 17571629, 63995561, 64742627, 65657914, 69613400, 38731273, 67911420, 39007615, 66583625, 65777235, 66782633, 66339926, 9904239, 21252244, 65506212, 65977068, 167623679, 64474525, 42272589, 36091865, 66752541, 67329767, 65477380, 167990362, 65626218, 67968100, 67247141, 37858962, 33732979, 66744947, 20822927, 38249992, 67292411, 66053289, 13581456, 67383571, 166327905, 165823420, 67458415, 68373997, 10276368, 65669111, 70697066, 21053600, 66838239, 56890477, 33140401, 166036375] cellular amide metabolic process
GO:0019538 0.250 1.668 7.181e-03 0.100 478 113 [7655641, 64669875, 20323736, 33709212, 27212193, 38310093, 19107849, 29630217, 5141220, 17035162, 8283720, 60453073, 5645650, 65259195, 28829095, 165941560, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 168124483, 20132923, 11332141, 165850968, 16968363, 40487328, 38183434, 5365520, 15916898, 3492858, 4416015, 62054342, 41621220, 62224782, 23449836, 10593880, 36697039, 38302786, 23721515, 33208200, 30459755, 12493950, 31342205, 12690700, 21157792, 167568891, 8550179, 44182220, 3576806, 68927583, 4582849, 59885854, 64742627, 65657914, 28150928, 69613400, 38731273, 62403068, 67911420, 39007615, 13571532, 167394958, 66583625, 65777235, 66782633, 66339926, 12417159, 9904239, 21252244, 65506212, 65977068, 167623679, 64474525, 42272589, 167278898, 36091865, 66752541, 67329767, 65477380, 167990362, 65626218, 67968100, 165780748, 13570862, 67247141, 37858962, 33732979, 66744947, 20822927, 38249992, 67292411, 66053289, 13581456, 67383571, 166327905, ...] protein metabolic process
GO:0015980 0.438 1.664 2.622e-02 0.095 82 16 [18275642, 18523127, 28436439, 38175368, 27695037, 165850493, 21015292, 48678785, 22308764, 22252819, 20888570, 166541972, 22197507, 13570629, 64395219, 62073848] energy derivation by oxidation of organic compounds
GO:0000271 0.431 1.640 3.199e-02 0.104 80 16 [18275642, 18523127, 28436439, 38175368, 27695037, 165850493, 21015292, 48678785, 22308764, 22252819, 20888570, 166541972, 13570629, 64395219, 42102729, 167266455] polysaccharide biosynthetic process
GO:0005976 0.431 1.639 3.234e-02 0.098 86 16 [18275642, 18523127, 28436439, 38175368, 27695037, 165850493, 21015292, 48678785, 22308764, 22252819, 20888570, 166541972, 13570629, 64395219, 42102729, 167266455] polysaccharide metabolic process
GO:0044042 0.431 1.636 3.582e-02 0.094 85 16 [18275642, 18523127, 28436439, 38175368, 27695037, 165850493, 21015292, 48678785, 22308764, 22252819, 20888570, 166541972, 13570629, 64395219, 42102729, 167266455] glucan metabolic process
GO:0034637 0.431 1.616 3.794e-02 0.101 93 16 [18275642, 18523127, 28436439, 38175368, 27695037, 165850493, 21015292, 48678785, 22308764, 22252819, 20888570, 166541972, 13570629, 64395219, 42102729, 167266455] cellular carbohydrate biosynthetic process
GO:0005978 0.442 1.609 4.042e-02 0.100 69 14 [18275642, 18523127, 28436439, 38175368, 27695037, 165850493, 21015292, 48678785, 22308764, 22252819, 20888570, 166541972, 13570629, 64395219] glycogen biosynthetic process
GO:0006112 0.442 1.591 3.970e-02 0.106 74 14 [18275642, 18523127, 28436439, 38175368, 27695037, 165850493, 21015292, 48678785, 22308764, 22252819, 20888570, 166541972, 13570629, 64395219] energy reserve metabolic process
GO:0009141 0.252 1.536 3.323e-02 0.127 381 75 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4559493, 4737261, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 167526299, 32363526, 22187812, 1809293, 268176, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 5960044, 17046519, 63185681, 8200910, 65033516, 13585577, 52152229, 66492431, 63266944, 3512858, 30588025, 18134535, 64427981, 64182902, 8551124, 17564385, 4220178, 12867643, 18128369, 62102911, 65935692, 168089107, 17549174, 20853105, 62848403, 31709972, 62566960, 66846572, 51336959, 64346968, 55261886, 48298182, 62829929, 65218941, 64479173, 64978197, 3624425, 28234013, 6131330, 20745054, 46324053, 45981629, 5189919, 10876818, 21126143, 62809084, 63123662, 62098267] nucleoside triphosphate metabolic process
GO:0005996 0.301 1.530 4.798e-02 0.120 222 39 [4715355, 6997781, 80888632, 17583418, 10226000, 15860346, 30252792, 61635847, 8532970, 61982117, 166487064, 36454371, 839701, 12964871, 63236804, 5960044, 17046519, 61106614, 8200910, 65033516, 18134535, 63640418, 18128923, 54139955, 13176452, 63032818, 63596410, 64823101, 45349478, 166870254, 62405280, 62299040, 62445847, 62763786, 62109485, 55848589, 62216988, 21899103, 6131330] monosaccharide metabolic process
GO:0046034 0.252 1.524 3.400e-02 0.120 379 75 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4559493, 4737261, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 167526299, 32363526, 22187812, 1809293, 268176, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 5960044, 17046519, 63185681, 8200910, 65033516, 13585577, 52152229, 66492431, 63266944, 3512858, 30588025, 18134535, 64427981, 64182902, 8551124, 17564385, 4220178, 12867643, 18128369, 62102911, 65935692, 168089107, 17549174, 20853105, 62848403, 31709972, 62566960, 66846572, 51336959, 64346968, 55261886, 48298182, 62829929, 65218941, 64479173, 64978197, 3624425, 28234013, 6131330, 20745054, 46324053, 45981629, 5189919, 10876818, 21126143, 62809084, 63123662, 62098267] ATP metabolic process
GO:0009126 0.250 1.521 3.517e-02 0.118 409 76 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4559493, 4737261, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 167526299, 32363526, 22187812, 1809293, 268176, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 5960044, 17046519, 63185681, 8200910, 65033516, 13585577, 52152229, 66492431, 63266944, 3512858, 30588025, 18134535, 64427981, 64182902, 8551124, 17564385, 4220178, 12867643, 18128369, 62102911, 65935692, 168089107, 17549174, 20853105, 62848403, 31709972, 63180877, 62566960, 66846572, 51336959, 64346968, 55261886, 48298182, 62829929, 65218941, 64479173, 64978197, 3624425, 28234013, 6131330, 20745054, 46324053, 45981629, 5189919, 10876818, 21126143, 62809084, 63123662, 62098267] purine nucleoside monophosphate metabolic process
GO:0046939 0.253 1.520 3.500e-02 0.114 304 70 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4559493, 4737261, 45207415, 29629717, 33420375, 9654148, 23089117, 25933508, 167526299, 22187812, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 5960044, 17046519, 63185681, 8200910, 65033516, 13585577, 52152229, 66492431, 63266944, 3512858, 30588025, 18134535, 64427981, 64182902, 8551124, 17564385, 4220178, 18128369, 62102911, 65935692, 168089107, 17549174, 20853105, 62848403, 31709972, 62566960, 66846572, 51336959, 64346968, 55261886, 48298182, 62829929, 65218941, 64479173, 64978197, 3624425, 28234013, 6131330, 20745054, 46324053, 45981629, 5189919, 10876818, 21126143, 62809084, 63123662, 62098267] nucleotide phosphorylation
GO:0009132 0.253 1.514 3.803e-02 0.114 304 70 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4559493, 4737261, 45207415, 29629717, 33420375, 9654148, 23089117, 25933508, 167526299, 22187812, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 5960044, 17046519, 63185681, 8200910, 65033516, 13585577, 52152229, 66492431, 63266944, 3512858, 30588025, 18134535, 64427981, 64182902, 8551124, 17564385, 4220178, 18128369, 62102911, 65935692, 168089107, 17549174, 20853105, 62848403, 31709972, 62566960, 66846572, 51336959, 64346968, 55261886, 48298182, 62829929, 65218941, 64479173, 64978197, 3624425, 28234013, 6131330, 20745054, 46324053, 45981629, 5189919, 10876818, 21126143, 62809084, 63123662, 62098267] nucleoside diphosphate metabolic process
GO:0009150 0.247 1.513 3.662e-02 0.111 412 77 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4559493, 4737261, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 167526299, 32363526, 22187812, 1809293, 268176, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 5960044, 17046519, 63185681, 8200910, 65033516, 13585577, 52152229, 66492431, 63266944, 3512858, 30588025, 18134535, 64427981, 64182902, 8551124, 17564385, 4220178, 12867643, 18128369, 62102911, 65935692, 168089107, 17549174, 20853105, 62848403, 31709972, 63180877, 62356804, 62566960, 66846572, 51336959, 64346968, 55261886, 48298182, 62829929, 65218941, 64479173, 64978197, 3624425, 28234013, 6131330, 20745054, 46324053, 45981629, 5189919, 10876818, 21126143, 62809084, 63123662, 62098267] purine ribonucleotide metabolic process
GO:0009135 0.253 1.511 3.871e-02 0.108 302 70 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4559493, 4737261, 45207415, 29629717, 33420375, 9654148, 23089117, 25933508, 167526299, 22187812, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 5960044, 17046519, 63185681, 8200910, 65033516, 13585577, 52152229, 66492431, 63266944, 3512858, 30588025, 18134535, 64427981, 64182902, 8551124, 17564385, 4220178, 18128369, 62102911, 65935692, 168089107, 17549174, 20853105, 62848403, 31709972, 62566960, 66846572, 51336959, 64346968, 55261886, 48298182, 62829929, 65218941, 64479173, 64978197, 3624425, 28234013, 6131330, 20745054, 46324053, 45981629, 5189919, 10876818, 21126143, 62809084, 63123662, 62098267] purine nucleoside diphosphate metabolic process
GO:0072524 0.250 1.501 4.005e-02 0.111 305 71 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4559493, 4737261, 45207415, 29629717, 33420375, 9654148, 23089117, 25933508, 167526299, 22187812, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 5960044, 17046519, 63185681, 8200910, 65033516, 13585577, 52152229, 66492431, 63266944, 3512858, 30588025, 18134535, 64427981, 64182902, 8551124, 17564385, 4220178, 18128369, 62102911, 65935692, 168089107, 17549174, 20853105, 166574781, 62848403, 31709972, 62566960, 66846572, 51336959, 64346968, 55261886, 48298182, 62829929, 65218941, 64479173, 64978197, 3624425, 28234013, 6131330, 20745054, 46324053, 45981629, 5189919, 10876818, 21126143, 62809084, 63123662, 62098267] pyridine-containing compound metabolic process
GO:0006733 0.250 1.493 4.320e-02 0.112 305 71 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4559493, 4737261, 45207415, 29629717, 33420375, 9654148, 23089117, 25933508, 167526299, 22187812, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 5960044, 17046519, 63185681, 8200910, 65033516, 13585577, 52152229, 66492431, 63266944, 3512858, 30588025, 18134535, 64427981, 64182902, 8551124, 17564385, 4220178, 18128369, 62102911, 65935692, 168089107, 17549174, 20853105, 166574781, 62848403, 31709972, 62566960, 66846572, 51336959, 64346968, 55261886, 48298182, 62829929, 65218941, 64479173, 64978197, 3624425, 28234013, 6131330, 20745054, 46324053, 45981629, 5189919, 10876818, 21126143, 62809084, 63123662, 62098267] oxidoreduction coenzyme metabolic process
GO:0009123 0.242 1.477 4.381e-02 0.118 412 78 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4559493, 4737261, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 167526299, 32363526, 22187812, 1809293, 268176, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 5960044, 17046519, 63185681, 8200910, 65033516, 13585577, 52152229, 66492431, 63266944, 3512858, 30588025, 18134535, 64427981, 64182902, 8551124, 17564385, 4220178, 12867643, 18128369, 62102911, 65935692, 168089107, 17549174, 20853105, 62848403, 31709972, 63180877, 62566960, 66846572, 51336959, 64346968, 55261886, 48298182, 62829929, 167057179, 64066327, 65218941, 64479173, 64978197, 3624425, 28234013, 6131330, 20745054, 46324053, 45981629, 5189919, 10876818, 21126143, 62809084, 63123662, 62098267] nucleoside monophosphate metabolic process
GO:0019693 0.239 1.475 4.279e-02 0.116 416 79 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4559493, 4737261, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 167526299, 32363526, 22187812, 1809293, 268176, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 5960044, 17046519, 63185681, 8200910, 65033516, 13585577, 52152229, 66492431, 63266944, 3512858, 30588025, 18134535, 64427981, 64182902, 8551124, 17564385, 4220178, 12867643, 18128369, 62102911, 65935692, 168089107, 17549174, 20853105, 62848403, 31709972, 63180877, 62356804, 62566960, 66846572, 51336959, 64346968, 55261886, 48298182, 62829929, 167057179, 64066327, 65218941, 64479173, 64978197, 3624425, 28234013, 6131330, 20745054, 46324053, 45981629, 5189919, 10876818, 21126143, 62809084, 63123662, 62098267] ribose phosphate metabolic process
GO:0009259 0.239 1.471 4.584e-02 0.115 414 79 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4559493, 4737261, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 167526299, 32363526, 22187812, 1809293, 268176, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 5960044, 17046519, 63185681, 8200910, 65033516, 13585577, 52152229, 66492431, 63266944, 3512858, 30588025, 18134535, 64427981, 64182902, 8551124, 17564385, 4220178, 12867643, 18128369, 62102911, 65935692, 168089107, 17549174, 20853105, 62848403, 31709972, 63180877, 62356804, 62566960, 66846572, 51336959, 64346968, 55261886, 48298182, 62829929, 167057179, 64066327, 65218941, 64479173, 64978197, 3624425, 28234013, 6131330, 20745054, 46324053, 45981629, 5189919, 10876818, 21126143, 62809084, 63123662, 62098267] ribonucleotide metabolic process
GO:0044724 0.239 1.470 4.955e-02 0.112 336 79 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4559493, 4737261, 45207415, 4715355, 29629717, 33420375, 9654148, 23089117, 25933508, 167526299, 22187812, 63441836, 61635847, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 63505555, 5960044, 17046519, 63185681, 8200910, 65033516, 13585577, 52152229, 66492431, 63266944, 3512858, 30588025, 18134535, 64427981, 64182902, 8551124, 17564385, 4220178, 18128369, 62102911, 64823101, 65935692, 168089107, 17549174, 20853105, 62848403, 31709972, 63332989, 62445847, 62566960, 66846572, 51336959, 64346968, 55261886, 48298182, 62829929, 65218941, 62216988, 64479173, 64978197, 3624425, 28234013, 6131330, 20745054, 46324053, 45981629, 5189919, 10876818, 21126143, 62809084, 13605039, 63123662, 62098267, 62450924] single-organism carbohydrate catabolic process
GO:0016052 0.239 1.467 4.932e-02 0.111 339 79 [30875488, 17585926, 8107297, 14006785, 4543087, 8170293, 4559493, 4737261, 45207415, 4715355, 29629717, 33420375, 9654148, 23089117, 25933508, 167526299, 22187812, 63441836, 61635847, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 63505555, 5960044, 17046519, 63185681, 8200910, 65033516, 13585577, 52152229, 66492431, 63266944, 3512858, 30588025, 18134535, 64427981, 64182902, 8551124, 17564385, 4220178, 18128369, 62102911, 64823101, 65935692, 168089107, 17549174, 20853105, 62848403, 31709972, 63332989, 62445847, 62566960, 66846572, 51336959, 64346968, 55261886, 48298182, 62829929, 65218941, 62216988, 64479173, 64978197, 3624425, 28234013, 6131330, 20745054, 46324053, 45981629, 5189919, 10876818, 21126143, 62809084, 13605039, 63123662, 62098267, 62450924] carbohydrate catabolic process

In [42]:
bp_wt


Out[42]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0009081 -0.577 -1.936 0.006 0.131 47 10 [20839749, 51213068, 63289385, 51313098, 13442927, 165749819, 63235820, 63662802, 63648739, 63600850] branched-chain amino acid metabolic process
GO:0009082 -0.571 -1.659 0.035 0.365 41 7 [20839749, 51213068, 51313098, 63235820, 63662802, 63648739, 63600850] branched-chain amino acid biosynthetic process
GO:0050794 -0.610 -1.657 0.032 0.246 36 6 [165873031, 167750483, 59827295, 66251821, 37727049, 65993244] regulation of cellular process
GO:0019222 -0.612 -1.644 0.039 0.199 59 6 [61892960, 10631876, 59827295, 66251821, 37727049, 65993244] regulation of metabolic process

In [43]:
cc_rt


Out[43]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0044446 0.493 2.191 6.741e-04 0.005 169 25 [7655641, 64669875, 20323736, 33709212, 17035162, 8283720, 65259195, 23226729, 6962424, 15891127, 6288540, 20132923, 3492858, 41621220, 10593880, 44182220, 68927583, 59885854, 64742627, 65657914, 9904239, 21252244, 65477380, 38249992, 65669111] intracellular organelle part
GO:0015934 0.642 2.188 7.048e-04 0.003 63 12 [7655641, 64669875, 20323736, 33709212, 17035162, 8283720, 15891127, 41621220, 44182220, 59885854, 64742627, 38249992] large ribosomal subunit
GO:0044391 0.493 2.172 6.767e-04 0.002 159 25 [7655641, 64669875, 20323736, 33709212, 17035162, 8283720, 65259195, 23226729, 6962424, 15891127, 6288540, 20132923, 3492858, 41621220, 10593880, 44182220, 68927583, 59885854, 64742627, 65657914, 9904239, 21252244, 65477380, 38249992, 65669111] ribosomal subunit
GO:0042995 0.362 2.062 1.571e-04 0.004 269 57 [168171488, 167307068, 13580518, 13586931, 167570053, 62303301, 42831732, 64855697, 64780867, 62417891, 62405618, 62136808, 62719918, 62849941, 57751592, 52127537, 13574239, 48437829, 68252636, 62771320, 63144665, 167641590, 62619244, 62923262, 62926584, 166007447, 28438217, 63195134, 63275290, 63842059, 64065097, 66593668, 62002315, 167738934, 66403957, 62565570, 62396394, 11407241, 167337265, 167047560, 13589494, 165880634, 167438835, 67398658, 63489079, 166530730, 168112544, 166818826, 64573539, 168001411, 63911288, 63937175, 168185530, 168106741, 168173199, 166250719, 166636440] cell projection
GO:0044422 0.345 2.038 7.831e-04 0.004 402 67 [7655641, 64669875, 20323736, 33709212, 17035162, 8283720, 65259195, 23226729, 6962424, 15891127, 6288540, 20132923, 3492858, 168171488, 41621220, 167307068, 10593880, 13580518, 13586931, 167570053, 62303301, 42831732, 64855697, 64780867, 62417891, 62405618, 62136808, 62719918, 62849941, 13574239, 62771320, 63144665, 62619244, 62923262, 62926584, 28438217, 44182220, 62002315, 68927583, 167738934, 66403957, 11407241, 167337265, 167047560, 13589494, 59885854, 64742627, 167438835, 67398658, 63489079, 166530730, 168112544, 166818826, 64573539, 168001411, 63911288, 63937175, 65657914, 168185530, 168106741, 9904239, 21252244, 65477380, 38249992, 65669111, 168173199, 166250719] organelle part
GO:0044463 0.350 1.816 6.970e-03 0.019 229 42 [168171488, 167307068, 13580518, 13586931, 167570053, 62303301, 42831732, 64855697, 64780867, 62417891, 62405618, 62136808, 62719918, 62849941, 13574239, 62771320, 63144665, 62619244, 62923262, 62926584, 28438217, 62002315, 167738934, 66403957, 11407241, 167337265, 167047560, 13589494, 167438835, 67398658, 63489079, 166530730, 168112544, 166818826, 64573539, 168001411, 63911288, 63937175, 168185530, 168106741, 168173199, 166250719] cell projection part
GO:0005622 0.312 1.811 4.740e-03 0.018 306 63 [7655641, 64669875, 20323736, 33709212, 5730052, 10185112, 19107849, 29630217, 8974409, 5141220, 60453073, 5645650, 65259195, 28829095, 165941560, 26879329, 25902959, 20862748, 15891127, 4100571, 41621220, 23449836, 3884277, 61884939, 5753625, 30556349, 61893464, 44182220, 3576806, 59885854, 167619418, 64742627, 65657914, 63123377, 69613400, 38731273, 21252244, 64474525, 42272589, 36091865, 67329767, 65477380, 67968100, 37858962, 33732979, 66744947, 20822927, 38249992, 67292411, 67383571, 166327905, 165823420, 67458415, 68373997, 10276368, 65669111, 70697066, 21053600, 66838239, 56890477, 33140401, 13604374, 29262834] intracellular
GO:1990904 0.272 1.742 4.833e-03 0.025 360 95 [7655641, 64669875, 20323736, 33709212, 19107849, 29630217, 5141220, 17035162, 8283720, 60453073, 5645650, 65259195, 28829095, 165941560, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 11332141, 165850968, 16968363, 40487328, 38183434, 5365520, 15916898, 3492858, 62054342, 41621220, 62224782, 23449836, 10593880, 36697039, 38302786, 23721515, 33208200, 30459755, 12493950, 31342205, 12690700, 44182220, 3576806, 68927583, 4582849, 59885854, 64742627, 65657914, 69613400, 38731273, 67911420, 39007615, 66583625, 65777235, 66782633, 9904239, 21252244, 65506212, 65977068, 167623679, 64474525, 42272589, 36091865, 66752541, 67329767, 65477380, 167990362, 65626218, 67968100, 67247141, 37858962, 33732979, 66744947, 20822927, 38249992, 67292411, 66053289, 13581456, 67383571, 166327905, 165823420, 67458415, 68373997, 10276368, 65669111, 70697066, 21053600, 66838239, 56890477, 33140401, 166036375] ribonucleoprotein complex
GO:0098796 0.523 1.598 4.273e-02 0.058 171 9 [1994037, 32363526, 1809293, 268176, 12867643, 47513944, 37969849, 63374013, 28273397] membrane protein complex
GO:0044444 0.216 1.448 4.363e-02 0.102 422 117 [7655641, 64669875, 20323736, 33709212, 29629717, 19107849, 29630217, 5141220, 17035162, 8283720, 23089117, 60453073, 5645650, 65259195, 28829095, 165941560, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 11332141, 165850968, 16968363, 40487328, 38183434, 5365520, 15916898, 3492858, 80889105, 62054342, 41621220, 62224782, 23449836, 10593880, 36697039, 38302786, 23721515, 33208200, 30459755, 12493950, 31342205, 12690700, 44182220, 22519241, 3576806, 68927583, 43045244, 4582849, 65221038, 17564385, 59885854, 64742627, 65657914, 63672434, 69613400, 38731273, 17549174, 67911420, 39007615, 20853105, 66583625, 65777235, 66782633, 62848403, 31709972, 9904239, 21252244, 65506212, 65977068, 167623679, 64474525, 42272589, 62566960, 36091865, 66752541, 67329767, 65477380, 167990362, 65626218, 67968100, 67247141, 37858962, 33732979, 66744947, 20822927, 38249992, 67292411, 66053289, 13581456, 67383571, 166327905, 165823420, 67458415, 68373997, ...] cytoplasmic part

In [44]:
cc_wt


Out[44]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0000015 -0.577 -2.341 0.000e+00 5.354e-04 43 16 [29629717, 23089117, 17564385, 17549174, 20853105, 62848403, 31709972, 62566960, 3624425, 20745054, 46324053, 45981629, 5189919, 10876818, 21126143, 62809084] phosphopyruvate hydratase complex
GO:0044445 -0.565 -2.333 2.360e-04 3.407e-04 47 17 [29629717, 23089117, 17564385, 63672434, 17549174, 20853105, 62848403, 31709972, 62566960, 3624425, 20745054, 46324053, 45981629, 5189919, 10876818, 21126143, 62809084] cytosolic part
GO:1902494 -0.468 -2.254 2.496e-04 4.542e-04 202 26 [29629717, 23089117, 11310502, 22519241, 43045244, 65221038, 17564385, 47513944, 37969849, 63374013, 17549174, 20853105, 28273397, 62848403, 31709972, 63401624, 62566960, 3624425, 20745054, 46324053, 45981629, 5189919, 10876818, 21126143, 62809084, 13571215] catalytic complex
GO:0016020 -0.391 -1.604 4.121e-02 3.126e-02 75 17 [21357752, 21687303, 62114668, 64265900, 46871761, 63823493, 167156307, 61699598, 166216926, 62830069, 27635679, 64013758, 166593522, 61660751, 65386242, 167150261, 165685567] membrane

RT vs Rag Human/Mouse


In [45]:
out_dir = "RT_Rag_hm_gsea"
df = pd.read_csv(os.path.join(BASE,"RT_Rag_deseq_results.csv"))
df = df[(df.padj.abs()<=0.2)]
df = df[df.human_mouse]
df['log2FoldChange'] = -1 * df['log2FoldChange']
rank_df = df[['Unnamed: 0', 'log2FoldChange']].rename(columns={'Unnamed: 0': 'gene_name', 'log2FoldChange': 'rank'})
rank_df = rank_df.sort_values('rank').reset_index(drop=True)
mf_res = run_go_gsea(rank_df, mf_map_f, seed=1111, outdir=out_dir)
bp_res = run_go_gsea(rank_df, bp_map_f, seed=1111, outdir=out_dir)
mf_rt = mf_res.query('nes > 0 and pval < 0.05').sort_values('nes', ascending=False)
mf_rag = mf_res.query('nes < 0 and pval < 0.05').sort_values('nes', ascending=True)
bp_rt = bp_res.query('nes > 0 and pval < 0.05').sort_values('nes', ascending=False)
bp_rag = bp_res.query('nes < 0 and pval < 0.05').sort_values('nes', ascending=True)


2017-04-04 12:48:56,283 Parsing data files for GSEA.............................
/usr/lib/python3/dist-packages/numpy/lib/arraysetops.py:379: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
  mask |= (ar1 == a)
2017-04-04 12:48:56,334 0008 gene_sets used for further statistical testing.....
2017-04-04 12:48:56,335 Start to run GSEA...Might take a while..................
2017-04-04 12:48:57,418 Start to generate gseapy reports, and produce figures...
/usr/lib/python3/dist-packages/matplotlib/figure.py:1744: UserWarning: This figure includes Axes that are not compatible with tight_layout, so its results might be incorrect.
  warnings.warn("This figure includes Axes that are not "
2017-04-04 12:48:59,534 Congratulations...GSEAPY run successfully...............
2017-04-04 12:48:59,552 Parsing data files for GSEA.............................
2017-04-04 12:48:59,606 0013 gene_sets used for further statistical testing.....
2017-04-04 12:48:59,607 Start to run GSEA...Might take a while..................
2017-04-04 12:49:01,499 Start to generate gseapy reports, and produce figures...
2017-04-04 12:49:04,846 Congratulations...GSEAPY run successfully...............

In [46]:
mf_rt


Out[46]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0008270 0.654 1.551 0.034 0.257 89 6 [165648111, 165648112, 61533297, 165637224, 61507483, 61501312] zinc ion binding

In [47]:
mf_rag


Out[47]:
es nes pval fdr gene_set_size matched_size genes name
Term

In [48]:
bp_rt


Out[48]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0065007 0.612 1.788 0.003 0.051 86 13 [165648111, 165648112, 61499238, 61499613, 61503068, 165636196, 165642139, 165646068, 165661488, 61457133, 61499612, 165666724, 165661076] biological regulation
GO:0050789 0.653 1.741 0.007 0.042 80 9 [165648111, 165648112, 61499238, 61503068, 165636196, 165642139, 165646068, 61457133, 165666724] regulation of biological process

In [49]:
bp_rag


Out[49]:
es nes pval fdr gene_set_size matched_size genes name
Term

RT vs Rag Non-Human/Mouse


In [50]:
out_dir = "RT_Rag_gsea"
df = pd.read_csv(os.path.join(BASE,"RT_Rag_deseq_results.csv"))
df = df[(df.padj.abs()<=0.2)]
df = df[~df.human_mouse]
df['log2FoldChange'] = -1 * df['log2FoldChange']
rank_df = df[['Unnamed: 0', 'log2FoldChange']].rename(columns={'Unnamed: 0': 'gene_name', 'log2FoldChange': 'rank'})
rank_df = rank_df.sort_values('rank').reset_index(drop=True)

In [51]:
mf_res = run_go_gsea(rank_df, mf_map_f, seed=1111, outdir=out_dir)
bp_res = run_go_gsea(rank_df, bp_map_f, seed=1111, outdir=out_dir)
cc_res = run_go_gsea(rank_df, cc_map_f, seed=1111, outdir=out_dir)
mf_rt = mf_res.query('nes > 0 and pval < 0.05').sort_values('nes', ascending=False)
mf_rag = mf_res.query('nes < 0 and pval < 0.05').sort_values('nes', ascending=True)
bp_rt = bp_res.query('nes > 0 and pval < 0.05').sort_values('nes', ascending=False)
bp_rag = bp_res.query('nes < 0 and pval < 0.05').sort_values('nes', ascending=True)
cc_rt = cc_res.query('nes > 0 and pval < 0.05').sort_values('nes', ascending=False)
cc_rag = cc_res.query('nes < 0 and pval < 0.05').sort_values('nes', ascending=True)


2017-04-04 12:49:05,166 Parsing data files for GSEA.............................
/usr/lib/python3/dist-packages/numpy/lib/arraysetops.py:379: FutureWarning: elementwise comparison failed; returning scalar instead, but in the future will perform elementwise comparison
  mask |= (ar1 == a)
2017-04-04 12:49:05,444 0077 gene_sets used for further statistical testing.....
2017-04-04 12:49:05,445 Start to run GSEA...Might take a while..................
2017-04-04 12:50:49,431 Start to generate gseapy reports, and produce figures...
/usr/lib/python3/dist-packages/matplotlib/figure.py:1744: UserWarning: This figure includes Axes that are not compatible with tight_layout, so its results might be incorrect.
  warnings.warn("This figure includes Axes that are not "
2017-04-04 12:50:55,293 Congratulations...GSEAPY run successfully...............
2017-04-04 12:50:55,313 Parsing data files for GSEA.............................
2017-04-04 12:50:55,626 0090 gene_sets used for further statistical testing.....
2017-04-04 12:50:55,627 Start to run GSEA...Might take a while..................
2017-04-04 12:53:12,328 Start to generate gseapy reports, and produce figures...
2017-04-04 12:53:18,305 Congratulations...GSEAPY run successfully...............
2017-04-04 12:53:18,312 Parsing data files for GSEA.............................
2017-04-04 12:53:18,381 0027 gene_sets used for further statistical testing.....
2017-04-04 12:53:18,382 Start to run GSEA...Might take a while..................
2017-04-04 12:54:00,362 Start to generate gseapy reports, and produce figures...
2017-04-04 12:54:06,269 Congratulations...GSEAPY run successfully...............

In [52]:
mf_rt


Out[52]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0016781 0.530 3.223 0.000e+00 0.000e+00 302 195 [61708790, 61884808, 36565362, 61724660, 51077372, 52166470, 61735080, 61731944, 10439591, 10550160, 36213075, 20333280, 7539645, 10899544, 11983619, 1654966, 7971161, 2550329, 2717161, 3723795, 64511620, 65325384, 6852416, 17374966, 33165099, 7297234, 39495835, 42033080, 45464484, 40105724, 61736606, 45577963, 67215245, 66119965, 12153742, 61721447, 42801234, 42222587, 166305458, 45352916, 31262207, 55837820, 36616158, 61723254, 14693091, 61792464, 7200027, 16289890, 7114893, 61686338, 21361007, 61722089, 51148156, 61731522, 61736645, 33383509, 6343409, 15304368, 9050982, 8071617, 6702801, 21125442, 20673079, 7309750, 7477105, 52796995, 21786113, 17395074, 6186763, 4228803, 3545035, 61725747, 6637923, 21265599, 8033819, 22855681, 26027080, 18675504, 10235090, 10296556, 10630096, 11072872, 29952533, 15038592, 15339324, 15551744, 32548173, 15894944, 32633754, 16859845, 30581852, 18127587, 31357883, 8541815, 3902762, 8042238, 2749207, 4246480, 4841345, 4854118, ...] phosphotransferase activity, paired acceptors
GO:0003723 0.663 3.209 0.000e+00 0.000e+00 367 55 [7655641, 64669875, 20323736, 33709212, 5141220, 8283720, 17035162, 52960359, 10185112, 8974409, 23226729, 6962424, 5730052, 15891127, 29630113, 23720124, 8107184, 20132923, 40487328, 16968363, 38183434, 15916898, 5365520, 61892960, 4100571, 3492858, 26879329, 41621220, 62224782, 10593880, 36697039, 61884939, 23721515, 38302786, 33208200, 12493950, 30459755, 31342205, 12690700, 10631876, 67469358, 66402327, 68927583, 5753625, 30556349, 61780119, 65259195, 21408386, 167619418, 65777235, 62322368, 166720030, 10899352, 29262834, 65669111] RNA binding
GO:0097747 0.621 3.010 0.000e+00 0.000e+00 345 55 [12999155, 23375966, 6243639, 16965124, 18068412, 61596152, 61782419, 4493173, 9867739, 21360327, 61595514, 74304202, 61719675, 48895505, 52385306, 6752061, 17299375, 62892851, 63204893, 8860974, 17354404, 8187869, 6675473, 6211757, 40202302, 10193140, 62063123, 52349047, 52155195, 64978053, 62155980, 61696438, 61687871, 41455330, 61761062, 41165392, 62823286, 63261481, 62902575, 66762307, 62874585, 62315770, 37387955, 51691431, 166882954, 43146673, 61079203, 21252862, 21868198, 7691951, 60772420, 56745534, 50065172, 44186767, 16841057] RNA polymerase activity
GO:0003677 0.583 2.844 0.000e+00 0.000e+00 369 58 [12999155, 23375966, 6243639, 16965124, 18068412, 61596152, 61782419, 4493173, 9867739, 21360327, 61595514, 74304202, 61719675, 48895505, 52385306, 6752061, 17299375, 62892851, 63204893, 8860974, 17354404, 8187869, 6675473, 6211757, 40202302, 10193140, 62063123, 52349047, 52155195, 64978053, 62155980, 61696438, 61687871, 41455330, 61761062, 41165392, 62823286, 63261481, 62902575, 66762307, 62874585, 62315770, 37387955, 51691431, 166882954, 43146673, 61079203, 21252862, 21868198, 7691951, 60772420, 56745534, 50065172, 44186767, 62437043, 46260937, 51907206, 16841057] DNA binding
GO:0016779 0.559 2.839 0.000e+00 0.000e+00 463 67 [12999155, 23375966, 6243639, 18275642, 61892960, 16965124, 10631876, 18068412, 61596152, 61782419, 4493173, 9867739, 21360327, 61595514, 74304202, 61719675, 48895505, 52385306, 6752061, 17299375, 62892851, 63204893, 8860974, 17354404, 8187869, 6675473, 6211757, 40202302, 10193140, 62063123, 52349047, 52155195, 64978053, 62155980, 61696438, 61687871, 41455330, 61761062, 41165392, 62823286, 63261481, 62902575, 66762307, 62874585, 62315770, 37387955, 51691431, 166882954, 43146673, 61780119, 61079203, 21252862, 21868198, 7691951, 60772420, 56745534, 50065172, 44186767, 13570629, 62718684, 59156012, 63039326, 63112646, 65657046, 57028376, 40551040, 16841057] nucleotidyltransferase activity
GO:0016301 0.433 2.667 0.000e+00 0.000e+00 480 207 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 33420375, 22187812, 61635847, 67028544, 61499980, 14397111, 59725586, 54913980, 3884277, 17583418, 61708790, 61884808, 61724660, 52166470, 61735080, 61731944, 10439591, 10550160, 20333280, 7539645, 10899544, 11983619, 1654966, 7971161, 2550329, 2717161, 3723795, 64511620, 65325384, 6852416, 17374966, 33165099, 7297234, 39495835, 42033080, 45464484, 40105724, 61736606, 45577963, 49792085, 12153742, 61721447, 45352916, 31262207, 61723254, 14693091, 61792464, 7200027, 16289890, 7114893, 61686338, 21361007, 61722089, 51148156, 61731522, 61736645, 33383509, 6343409, 15304368, 9050982, 8071617, 6702801, 21125442, 20673079, 7309750, 7477105, 52796995, 21786113, 17395074, 6186763, 4228803, 3545035, 61725747, 6637923, 21265599, 8033819, 22855681, 26027080, 18675504, 10235090, 10296556, 10630096, 11072872, 29952533, 15038592, 15339324, 15551744, 32548173, 15894944, 32633754, 16859845, ...] kinase activity
GO:0004618 0.727 2.640 0.000e+00 0.000e+00 78 19 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 33420375, 22187812, 67028544, 59725586, 54913980, 4220178, 62754658, 65935692, 168089107, 63123662] phosphoglycerate kinase activity
GO:0001882 0.578 2.562 0.000e+00 0.000e+00 398 38 [5888442, 80382425, 21138590, 69205977, 10185112, 32794085, 40640683, 12999155, 8974409, 23375966, 6243639, 5730052, 12661961, 4100571, 36454371, 26879329, 61884939, 69572327, 49556056, 61982117, 15782696, 36608698, 61106614, 5753625, 27263339, 80394470, 15769577, 67719393, 30556349, 166882954, 43146673, 167619418, 20215972, 66609079, 69425997, 29262834, 3557492, 40723118] nucleoside binding
GO:0016774 0.626 2.414 0.000e+00 1.213e-05 111 23 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 33420375, 22187812, 67028544, 59725586, 54913980, 3884277, 4220178, 62754658, 63035046, 65935692, 168089107, 45593936, 13604374, 63123662] phosphotransferase activity, carboxyl group as acceptor
GO:0001883 0.562 2.404 0.000e+00 1.092e-05 248 33 [5888442, 80382425, 21138590, 69205977, 10185112, 32794085, 40640683, 8974409, 5730052, 12661961, 4100571, 36454371, 26879329, 61884939, 69572327, 49556056, 61982117, 15782696, 36608698, 61106614, 5753625, 27263339, 80394470, 15769577, 67719393, 30556349, 167619418, 20215972, 66609079, 69425997, 29262834, 3557492, 40723118] purine nucleoside binding
GO:0003735 0.446 2.403 0.000e+00 9.928e-06 360 91 [7655641, 64669875, 20323736, 33709212, 66453589, 67144272, 19107849, 29630217, 5141220, 8283720, 17035162, 60453073, 5645650, 28829095, 165941560, 3576806, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 40487328, 16968363, 38183434, 15916898, 5365520, 3492858, 41621220, 62224782, 10593880, 23449836, 36697039, 23721515, 38302786, 33208200, 12493950, 30459755, 31342205, 12690700, 67469358, 3497381, 6962421, 65977279, 66402327, 68927583, 65259195, 21408386, 65777235, 20720618, 66350717, 66050469, 65886657, 66541818, 67061811, 168017014, 166807349, 7259645, 29341916, 67389484, 74406712, 82054302, 48590768, 167340047, 4774708, 166720030, 67911420, 64474525, 39007615, 42272589, 167990362, 66752541, 10899352, 167349682, 67383571, 65506212, 65977068, 65626218, 167623679, 38249992, 67911893, 67774188, 4009201, 166036375, 65669111, 10276368, 13581456] structural constituent of ribosome
GO:0019001 0.562 2.399 0.000e+00 9.101e-06 248 33 [5888442, 80382425, 21138590, 69205977, 10185112, 32794085, 40640683, 8974409, 5730052, 12661961, 4100571, 36454371, 26879329, 61884939, 69572327, 49556056, 61982117, 15782696, 36608698, 61106614, 5753625, 27263339, 80394470, 15769577, 67719393, 30556349, 167619418, 20215972, 66609079, 69425997, 29262834, 3557492, 40723118] guanyl nucleotide binding
GO:0000287 0.528 2.226 3.329e-04 1.764e-04 113 32 [29629717, 9654148, 23089117, 25933508, 17589318, 26904631, 27290903, 29001612, 7496609, 20853009, 29983272, 28314259, 66137094, 17549174, 23090099, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 22196542, 62198791, 62071220, 62150865, 63648739, 63662802, 62176760, 62566960, 39279903] magnesium ion binding
GO:0022892 0.601 2.144 6.887e-04 6.552e-04 89 18 [3885199, 1994037, 29978920, 33721585, 38210955, 54503535, 21357752, 32363526, 1809293, 268176, 21432496, 13568664, 65627086, 62354250, 27807827, 62344870, 165706474, 62660497] substrate-specific transporter activity
GO:0004634 0.645 2.118 5.187e-04 9.537e-04 43 14 [29629717, 23089117, 66137094, 17549174, 23090099, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 62566960] phosphopyruvate hydratase activity
GO:0004347 0.764 1.986 5.461e-04 3.501e-03 43 7 [839701, 12964871, 5960044, 17046519, 8200910, 65033516, 62446788] glucose-6-phosphate isomerase activity
GO:0016829 0.398 1.936 4.728e-04 5.467e-03 279 56 [29629717, 23089117, 21276719, 51212653, 63441836, 55408710, 48323766, 80889105, 19508028, 36454371, 21164095, 66137094, 17549174, 44157917, 66272695, 23090099, 61982117, 167691730, 68152818, 48634285, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 61106614, 21269278, 62887295, 40267857, 62783504, 46503123, 15545077, 54789106, 66236977, 64427981, 37225500, 49673151, 63649356, 63517822, 29774394, 68084246, 47787704, 166165052, 63157973, 62217311, 22196793, 15754209, 166574781, 51262100, 57701171, 13191330, 62566960, 20625233, 62356804, 64479173] lyase activity
GO:0016614 0.475 1.886 4.508e-03 8.112e-03 150 26 [13684061, 6155443, 11147909, 16967630, 56134344, 26904631, 27290903, 29001612, 16965587, 7496609, 20853009, 29983272, 12905190, 10318713, 62274246, 20839749, 61686088, 7011122, 63296313, 63332989, 166616289, 63863560, 63648739, 63662802, 61717636, 167277486] oxidoreductase activity, acting on CH-OH group of donors
GO:0016835 0.484 1.794 9.816e-03 1.720e-02 85 20 [29629717, 23089117, 80889105, 66137094, 17549174, 23090099, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 66236977, 37225500, 62217311, 51262100, 57701171, 62566960] carbon-oxygen lyase activity
GO:0070279 0.510 1.783 1.032e-02 1.809e-02 136 17 [10968755, 166738288, 55061408, 21276719, 51212653, 55408710, 48323766, 61748514, 167871404, 61739923, 55719313, 37097543, 40564648, 61729631, 21812180, 61791542, 46701851] vitamin B6 binding
GO:0008135 0.571 1.691 2.241e-02 3.555e-02 74 10 [10185112, 8974409, 5730052, 4100571, 26879329, 61884939, 5753625, 30556349, 167619418, 29262834] translation factor activity, RNA binding
GO:0016860 0.406 1.628 2.264e-02 5.266e-02 139 27 [4715355, 80888632, 10226000, 30252792, 61635847, 8532970, 30623941, 839701, 12964871, 5960044, 17046519, 8200910, 65033516, 30588025, 62446788, 62209062, 62907054, 63167857, 62199335, 65811933, 64380885, 67494413, 55529526, 6961308, 40586201, 8455053, 64978197] intramolecular oxidoreductase activity
GO:0016831 0.528 1.622 3.036e-02 5.257e-02 88 11 [21276719, 51212653, 55408710, 48323766, 36454371, 61982117, 61106614, 54789106, 49673151, 22196793, 15754209] carboxy-lyase activity
GO:0015078 0.583 1.595 3.457e-02 5.997e-02 64 8 [1994037, 32363526, 1809293, 268176, 13568664, 65627086, 62354250, 62344870] hydrogen ion transmembrane transporter activity
GO:0043492 0.583 1.593 3.729e-02 5.843e-02 67 8 [1994037, 32363526, 1809293, 268176, 13568664, 65627086, 62354250, 62344870] ATPase activity, coupled to movement of substances
GO:0015399 0.583 1.593 4.094e-02 5.627e-02 67 8 [1994037, 32363526, 1809293, 268176, 13568664, 65627086, 62354250, 62344870] primary active transmembrane transporter activity
GO:0044769 0.583 1.590 4.192e-02 5.489e-02 64 8 [1994037, 32363526, 1809293, 268176, 13568664, 65627086, 62354250, 62344870] ATPase activity, coupled to transmembrane movement of ions, rotational mechanism
GO:0042623 0.583 1.589 4.277e-02 5.345e-02 68 8 [1994037, 32363526, 1809293, 268176, 13568664, 65627086, 62354250, 62344870] ATPase activity, coupled
GO:0016830 0.366 1.582 3.094e-02 5.426e-02 161 34 [21276719, 51212653, 63441836, 55408710, 48323766, 19508028, 36454371, 21164095, 66272695, 61982117, 167691730, 68152818, 48634285, 61106614, 21269278, 40267857, 46503123, 15545077, 54789106, 64427981, 49673151, 63649356, 63517822, 29774394, 68084246, 47787704, 166165052, 63157973, 22196793, 15754209, 166574781, 13191330, 20625233, 64479173] carbon-carbon lyase activity

In [53]:
mf_rag


Out[53]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0009055 -0.646 -2.467 0.000 4.325e-04 38 18 [63507869, 63623628, 64864375, 63379850, 64572991, 62942791, 64649656, 49911241, 45703293, 61957888, 21346720, 63079626, 6263025, 63389326, 21834593, 64646230, 63098496, 167701862] electron carrier activity
GO:0051540 -0.597 -2.403 0.000 3.892e-04 149 21 [80889105, 61600538, 61963309, 61598826, 64109059, 61600015, 58687019, 62139539, 48340027, 61601993, 168109762, 57602627, 61621955, 61957888, 21346720, 62751142, 167701862, 167744672, 63901915, 61608244, 166278783] metal cluster binding
GO:0016887 -0.411 -2.327 0.000 5.190e-04 249 73 [1994037, 32363526, 1809293, 268176, 13568664, 63078357, 63959850, 6924770, 63452797, 77351967, 43878788, 67306374, 13441580, 10689069, 66551099, 47459480, 56069133, 63684566, 15207893, 28360306, 63332162, 17587826, 63205501, 32955361, 5247630, 6347838, 14468787, 31357673, 32157942, 13841186, 13203808, 62946388, 28669498, 61865720, 63129880, 65627086, 63468226, 9085008, 63133221, 20629788, 64420003, 67347833, 63199719, 63281680, 12378604, 40686252, 62354250, 168161151, 66854840, 40674602, 28240379, 63132923, 62545344, 167915219, 45006276, 28273397, 29219301, 62344870, 11992086, 10265600, 17618404, 56076521, 66939789, 13413281, 29505496, 9507913, 22209574, 31262467, 33706145, 63301199, 13842682, 63695501, 63374013] ATPase activity
GO:0016820 -0.366 -1.940 0.001 2.104e-02 190 56 [1994037, 32363526, 1809293, 268176, 13568664, 63078357, 6924770, 63452797, 77351967, 10689069, 15207893, 28360306, 63332162, 17587826, 63205501, 32955361, 6347838, 31357673, 32157942, 13841186, 13203808, 62946388, 28669498, 61865720, 63129880, 65627086, 63468226, 63133221, 20629788, 63199719, 12378604, 40686252, 62354250, 168161151, 65516796, 40674602, 28240379, 66978191, 63132923, 62545344, 167915219, 165851092, 28273397, 47513944, 62344870, 11992086, 10265600, 17618404, 56076521, 13413281, 29505496, 22209574, 31262467, 33706145, 37969849, 63374013] hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances
GO:1901681 -0.574 -1.801 0.012 4.704e-02 80 10 [3740901, 61600538, 61598826, 61600015, 61601993, 168109762, 57602627, 61621955, 61608244, 166278783] sulfur compound binding
GO:0030976 -0.574 -1.790 0.015 4.238e-02 79 10 [3740901, 61600538, 61598826, 61600015, 61601993, 168109762, 57602627, 61621955, 61608244, 166278783] thiamine pyrophosphate binding
GO:0005215 -0.305 -1.790 0.001 3.641e-02 256 83 [3885199, 1994037, 29978920, 33721585, 38210955, 54503535, 21357752, 32363526, 1809293, 268176, 21432496, 13568664, 63078357, 6924770, 63452797, 77351967, 10689069, 15207893, 28360306, 63332162, 17587826, 63205501, 32955361, 6347838, 31357673, 32157942, 13841186, 13203808, 62946388, 28669498, 61865720, 63129880, 65627086, 63468226, 63133221, 20629788, 63199719, 12378604, 40686252, 62354250, 168161151, 13571500, 65516796, 40674602, 28240379, 66978191, 63132923, 62545344, 167915219, 165851092, 28273397, 47513944, 167285315, 13587543, 166593522, 167348034, 166208277, 27807827, 167156307, 62344870, 11992086, 10265600, 17618404, 56076521, 13570595, 13413281, 29505496, 22209574, 31262467, 33706145, 37969849, 63374013, 28423332, 166294804, 29374081, 165685567, 11412988, 167645582, 165706474, 62660497, 167399046, 165992613, 167279298] transporter activity
GO:0022804 -0.321 -1.755 0.006 4.083e-02 205 61 [1994037, 33721585, 21357752, 32363526, 1809293, 268176, 13568664, 63078357, 6924770, 63452797, 77351967, 10689069, 15207893, 28360306, 63332162, 17587826, 63205501, 32955361, 6347838, 31357673, 32157942, 13841186, 13203808, 62946388, 28669498, 61865720, 63129880, 65627086, 63468226, 63133221, 20629788, 63199719, 12378604, 40686252, 62354250, 168161151, 65516796, 40674602, 28240379, 66978191, 63132923, 62545344, 167915219, 165851092, 28273397, 47513944, 27807827, 62344870, 11992086, 10265600, 17618404, 56076521, 13413281, 29505496, 22209574, 31262467, 33706145, 37969849, 63374013, 165706474, 62660497] active transmembrane transporter activity
GO:0016757 -0.521 -1.750 0.016 3.743e-02 79 12 [13750734, 61748514, 167871404, 61739923, 55719313, 37097543, 40564648, 61729631, 166574781, 21812180, 61791542, 167284707] transferase activity, transferring glycosyl groups
GO:0016758 -0.560 -1.737 0.022 3.685e-02 76 10 [61748514, 167871404, 61739923, 55719313, 37097543, 40564648, 61729631, 21812180, 61791542, 167284707] transferase activity, transferring hexosyl groups
GO:0050660 -0.554 -1.729 0.022 3.534e-02 43 10 [63507869, 63623628, 64864375, 7011122, 166616289, 63379850, 62942791, 48540155, 63389326, 62304018] flavin adenine dinucleotide binding
GO:0004645 -0.559 -1.682 0.027 4.380e-02 55 9 [61748514, 167871404, 61739923, 55719313, 37097543, 40564648, 61729631, 21812180, 61791542] phosphorylase activity
GO:0016817 -0.252 -1.526 0.013 9.946e-02 454 97 [1994037, 10185112, 8974409, 32363526, 5730052, 1809293, 268176, 4100571, 26879329, 28314259, 61884939, 49556056, 13568664, 15782696, 5753625, 27263339, 30556349, 167619418, 63078357, 63959850, 6924770, 63452797, 77351967, 43878788, 67306374, 13441580, 20215972, 10689069, 66551099, 47459480, 56069133, 63684566, 15207893, 28360306, 63332162, 17587826, 63205501, 32955361, 5247630, 6347838, 14468787, 31357673, 32157942, 13841186, 13203808, 62946388, 28669498, 61865720, 63129880, 65627086, 63468226, 9085008, 63133221, 20629788, 64420003, 67347833, 63199719, 63281680, 12378604, 40686252, 62354250, 168161151, 66609079, 66854840, 69425997, 65516796, 40674602, 28240379, 66978191, 63132923, 62545344, 167915219, 45006276, 165851092, 28273397, 47513944, 29219301, 62344870, 11992086, 10265600, 17618404, 56076521, 66939789, 13413281, 29505496, 9507913, 22209574, 31262467, 33706145, 63301199, 13842682, 37969849, 63695501, 63374013, 29262834, 3557492, 40723118] hydrolase activity, acting on acid anhydrides
GO:0016903 -0.293 -1.490 0.043 1.035e-01 282 48 [2478382, 733338, 51753038, 3740901, 36107728, 6997781, 11310565, 63371685, 43414939, 53279804, 10318713, 63640418, 62669104, 61600538, 62232545, 61963309, 61598826, 53586382, 64109059, 63571991, 59329815, 61600015, 61686088, 58687019, 62139539, 61986126, 50431192, 63603065, 45843396, 61901179, 63849179, 61717636, 62184180, 48340027, 61601993, 168109762, 61880488, 42221176, 166781730, 57602627, 44171740, 61621955, 45723591, 21899103, 62312164, 57098781, 61608244, 166278783] oxidoreductase activity, acting on the aldehyde or oxo group of donors
GO:0017111 -0.243 -1.438 0.033 1.262e-01 407 91 [1994037, 10185112, 8974409, 32363526, 5730052, 1809293, 268176, 4100571, 26879329, 61884939, 49556056, 13568664, 15782696, 5753625, 27263339, 30556349, 167619418, 63078357, 63959850, 6924770, 63452797, 77351967, 43878788, 67306374, 13441580, 20215972, 10689069, 66551099, 47459480, 56069133, 63684566, 15207893, 28360306, 63332162, 17587826, 63205501, 32955361, 5247630, 6347838, 14468787, 31357673, 32157942, 13841186, 13203808, 62946388, 28669498, 61865720, 63129880, 65627086, 63468226, 9085008, 63133221, 20629788, 64420003, 67347833, 63199719, 63281680, 12378604, 40686252, 62354250, 168161151, 66609079, 66854840, 69425997, 40674602, 28240379, 63132923, 62545344, 167915219, 45006276, 28273397, 29219301, 62344870, 11992086, 10265600, 17618404, 56076521, 66939789, 13413281, 29505496, 9507913, 22209574, 31262467, 33706145, 63301199, 13842682, 63695501, 63374013, 29262834, 3557492, 40723118] nucleoside-triphosphatase activity
GO:0016818 -0.229 -1.369 0.046 1.345e-01 438 92 [1994037, 10185112, 8974409, 32363526, 5730052, 1809293, 268176, 4100571, 26879329, 28314259, 61884939, 49556056, 13568664, 15782696, 5753625, 27263339, 30556349, 167619418, 63078357, 63959850, 6924770, 63452797, 77351967, 43878788, 67306374, 13441580, 20215972, 10689069, 66551099, 47459480, 56069133, 63684566, 15207893, 28360306, 63332162, 17587826, 63205501, 32955361, 5247630, 6347838, 14468787, 31357673, 32157942, 13841186, 13203808, 62946388, 28669498, 61865720, 63129880, 65627086, 63468226, 9085008, 63133221, 20629788, 64420003, 67347833, 63199719, 63281680, 12378604, 40686252, 62354250, 168161151, 66609079, 66854840, 69425997, 40674602, 28240379, 63132923, 62545344, 167915219, 45006276, 28273397, 29219301, 62344870, 11992086, 10265600, 17618404, 56076521, 66939789, 13413281, 29505496, 9507913, 22209574, 31262467, 33706145, 63301199, 13842682, 63695501, 63374013, 29262834, 3557492, 40723118] hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides

In [54]:
bp_rt


Out[54]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0032774 0.621 2.987 0.000e+00 0.000e+00 345 55 [12999155, 23375966, 6243639, 16965124, 18068412, 61596152, 61782419, 4493173, 9867739, 21360327, 61595514, 74304202, 61719675, 48895505, 52385306, 6752061, 17299375, 62892851, 63204893, 8860974, 17354404, 8187869, 6675473, 6211757, 40202302, 10193140, 62063123, 52349047, 52155195, 64978053, 62155980, 61696438, 61687871, 41455330, 61761062, 41165392, 62823286, 63261481, 62902575, 66762307, 62874585, 62315770, 37387955, 51691431, 166882954, 43146673, 61079203, 21252862, 21868198, 7691951, 60772420, 56745534, 50065172, 44186767, 16841057] RNA biosynthetic process
GO:0046034 0.509 2.566 0.000e+00 0.000e+00 379 66 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 32363526, 22187812, 1809293, 268176, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 66137094, 5960044, 17046519, 17549174, 8200910, 65033516, 23090099, 13568664, 30588025, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 3646533, 64427981, 4220178, 63649356, 62446788, 63517822, 65627086, 62748898, 62354250, 166499573, 62754658, 166165052, 63157973, 64380885, 65935692, 168089107, 62344870, 62566960, 165866251, 64479173, 62098267, 64978197, 63123662] ATP metabolic process
GO:0009141 0.509 2.565 0.000e+00 0.000e+00 381 66 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 32363526, 22187812, 1809293, 268176, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 66137094, 5960044, 17046519, 17549174, 8200910, 65033516, 23090099, 13568664, 30588025, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 3646533, 64427981, 4220178, 63649356, 62446788, 63517822, 65627086, 62748898, 62354250, 166499573, 62754658, 166165052, 63157973, 64380885, 65935692, 168089107, 62344870, 62566960, 165866251, 64479173, 62098267, 64978197, 63123662] nucleoside triphosphate metabolic process
GO:0009123 0.496 2.520 0.000e+00 0.000e+00 412 67 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 32363526, 22187812, 1809293, 268176, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 66137094, 5960044, 17046519, 17549174, 8200910, 65033516, 23090099, 13568664, 30588025, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 3646533, 64427981, 4220178, 63649356, 62446788, 63517822, 65627086, 62748898, 62354250, 166499573, 62754658, 166165052, 63157973, 64380885, 65935692, 168089107, 62344870, 62566960, 165866251, 63180877, 64479173, 62098267, 64978197, 63123662] nucleoside monophosphate metabolic process
GO:0009126 0.496 2.502 0.000e+00 2.613e-05 409 67 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 32363526, 22187812, 1809293, 268176, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 66137094, 5960044, 17046519, 17549174, 8200910, 65033516, 23090099, 13568664, 30588025, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 3646533, 64427981, 4220178, 63649356, 62446788, 63517822, 65627086, 62748898, 62354250, 166499573, 62754658, 166165052, 63157973, 64380885, 65935692, 168089107, 62344870, 62566960, 165866251, 63180877, 64479173, 62098267, 64978197, 63123662] purine nucleoside monophosphate metabolic process
GO:0009132 0.504 2.469 0.000e+00 4.355e-05 304 58 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 66137094, 5960044, 17046519, 17549174, 8200910, 65033516, 23090099, 30588025, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 3646533, 64427981, 4220178, 63649356, 62446788, 63517822, 62748898, 166499573, 62754658, 166165052, 63157973, 64380885, 65935692, 168089107, 62566960, 165866251, 64479173, 62098267, 64978197, 63123662] nucleoside diphosphate metabolic process
GO:0046939 0.504 2.463 0.000e+00 3.733e-05 304 58 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 66137094, 5960044, 17046519, 17549174, 8200910, 65033516, 23090099, 30588025, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 3646533, 64427981, 4220178, 63649356, 62446788, 63517822, 62748898, 166499573, 62754658, 166165052, 63157973, 64380885, 65935692, 168089107, 62566960, 165866251, 64479173, 62098267, 64978197, 63123662] nucleotide phosphorylation
GO:0044267 0.451 2.461 0.000e+00 3.266e-05 413 99 [7655641, 64669875, 20323736, 33709212, 66453589, 67144272, 27212193, 38310093, 19107849, 29630217, 5141220, 8283720, 17035162, 60453073, 5645650, 28829095, 165941560, 3576806, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 21157792, 20132923, 40487328, 16968363, 38183434, 15916898, 5365520, 3492858, 41621220, 62224782, 10593880, 23449836, 36697039, 23721515, 38302786, 33208200, 12493950, 30459755, 31342205, 12690700, 67469358, 3497381, 62120168, 6962421, 51629989, 48778871, 65977279, 66402327, 68927583, 65259195, 21408386, 62273450, 64990955, 65777235, 20720618, 66350717, 66050469, 65886657, 66541818, 67061811, 168017014, 166807349, 7259645, 29341916, 67389484, 74406712, 82054302, 48590768, 167340047, 4774708, 166720030, 67911420, 64474525, 39007615, 42272589, 167990362, 66752541, 10899352, 167349682, 67383571, 65506212, 65977068, 65626218, 167623679, 38249992, 67911893, 67774188, 4009201, 166036375, 65669111, 10276368, 13581456] cellular protein metabolic process
GO:0009135 0.504 2.458 0.000e+00 2.903e-05 302 58 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 66137094, 5960044, 17046519, 17549174, 8200910, 65033516, 23090099, 30588025, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 3646533, 64427981, 4220178, 63649356, 62446788, 63517822, 62748898, 166499573, 62754658, 166165052, 63157973, 64380885, 65935692, 168089107, 62566960, 165866251, 64479173, 62098267, 64978197, 63123662] purine nucleoside diphosphate metabolic process
GO:0009259 0.482 2.453 0.000e+00 2.613e-05 414 68 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 32363526, 22187812, 1809293, 268176, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 66137094, 5960044, 17046519, 17549174, 8200910, 65033516, 23090099, 13568664, 30588025, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 3646533, 64427981, 4220178, 63649356, 62446788, 63517822, 65627086, 62748898, 62354250, 166499573, 62754658, 166165052, 63157973, 64380885, 65935692, 168089107, 62344870, 62566960, 165866251, 63180877, 62356804, 64479173, 62098267, 64978197, 63123662] ribonucleotide metabolic process
GO:1901135 0.477 2.450 0.000e+00 3.563e-05 447 74 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 32363526, 22187812, 1809293, 268176, 63441836, 61635847, 67028544, 19508028, 59725586, 54913980, 30623941, 839701, 12964871, 21164095, 66137094, 5960044, 17046519, 17549174, 8200910, 65033516, 23090099, 13568664, 30588025, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 3646533, 64427981, 13750734, 4220178, 63649356, 62446788, 63517822, 65627086, 62748898, 62354250, 166499573, 62754658, 166165052, 63157973, 64380885, 65935692, 168089107, 63863560, 62344870, 51262100, 62566960, 165866251, 63180877, 62356804, 64479173, 62098267, 64978197, 63123662] carbohydrate derivative metabolic process
GO:0019538 0.441 2.446 0.000e+00 3.266e-05 478 105 [7655641, 64669875, 20323736, 33709212, 66453589, 67144272, 27212193, 38310093, 19107849, 29630217, 5141220, 8283720, 17035162, 60453073, 5645650, 28829095, 165941560, 3576806, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 21157792, 20132923, 40487328, 16968363, 38183434, 15916898, 5365520, 51277953, 3492858, 41621220, 62224782, 10593880, 23449836, 36697039, 23721515, 38302786, 33208200, 12493950, 30459755, 31342205, 12690700, 67469358, 3497381, 62120168, 6962421, 8550179, 167568891, 51629989, 48778871, 65977279, 66402327, 68927583, 65259195, 21408386, 62273450, 64990955, 65777235, 20720618, 66350717, 66050469, 65886657, 66541818, 67061811, 168017014, 166807349, 7259645, 29341916, 67389484, 74406712, 82054302, 48590768, 167340047, 4774708, 166720030, 67911420, 64474525, 39007615, 167394958, 42272589, 167990362, 66752541, 10899352, 167349682, 12417159, 67383571, 65506212, 65977068, 65626218, 167623679, 38249992, 67911893, 67774188, 4009201, ...] protein metabolic process
GO:0009150 0.482 2.443 0.000e+00 3.015e-05 412 68 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 32363526, 22187812, 1809293, 268176, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 66137094, 5960044, 17046519, 17549174, 8200910, 65033516, 23090099, 13568664, 30588025, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 3646533, 64427981, 4220178, 63649356, 62446788, 63517822, 65627086, 62748898, 62354250, 166499573, 62754658, 166165052, 63157973, 64380885, 65935692, 168089107, 62344870, 62566960, 165866251, 63180877, 62356804, 64479173, 62098267, 64978197, 63123662] purine ribonucleotide metabolic process
GO:0019693 0.476 2.425 0.000e+00 2.799e-05 416 69 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 32363526, 22187812, 1809293, 268176, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 66137094, 5960044, 17046519, 17549174, 8200910, 65033516, 23090099, 13568664, 30588025, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 3646533, 64427981, 4220178, 63649356, 62446788, 63517822, 65627086, 62748898, 62354250, 166499573, 62754658, 166165052, 63157973, 64380885, 65935692, 168089107, 63863560, 62344870, 62566960, 165866251, 63180877, 62356804, 64479173, 62098267, 64978197, 63123662] ribose phosphate metabolic process
GO:0006753 0.468 2.414 0.000e+00 2.613e-05 497 74 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 32363526, 22187812, 1809293, 268176, 63441836, 67028544, 19508028, 59725586, 54913980, 30623941, 839701, 12964871, 21164095, 66137094, 5960044, 17046519, 17549174, 8200910, 65033516, 23090099, 13568664, 30588025, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 3646533, 62274246, 64427981, 4220178, 63649356, 62446788, 63517822, 65627086, 62748898, 62354250, 63006542, 166499573, 62754658, 166165052, 63157973, 64380885, 65935692, 168089107, 63863560, 166574781, 62344870, 62566960, 165866251, 63180877, 62356804, 64479173, 62098267, 64978197, 63123662] nucleoside phosphate metabolic process
GO:0009117 0.468 2.408 0.000e+00 3.266e-05 496 74 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 32363526, 22187812, 1809293, 268176, 63441836, 67028544, 19508028, 59725586, 54913980, 30623941, 839701, 12964871, 21164095, 66137094, 5960044, 17046519, 17549174, 8200910, 65033516, 23090099, 13568664, 30588025, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 3646533, 62274246, 64427981, 4220178, 63649356, 62446788, 63517822, 65627086, 62748898, 62354250, 63006542, 166499573, 62754658, 166165052, 63157973, 64380885, 65935692, 168089107, 63863560, 166574781, 62344870, 62566960, 165866251, 63180877, 62356804, 64479173, 62098267, 64978197, 63123662] nucleotide metabolic process
GO:0072521 0.472 2.405 0.000e+00 3.074e-05 475 70 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 29629717, 33420375, 1994037, 9654148, 23089117, 25933508, 32363526, 22187812, 1809293, 268176, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 66137094, 5960044, 17046519, 17549174, 8200910, 65033516, 23090099, 13568664, 30588025, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 3646533, 62274246, 64427981, 4220178, 63649356, 62446788, 63517822, 65627086, 62748898, 62354250, 63006542, 166499573, 62754658, 166165052, 63157973, 64380885, 65935692, 168089107, 62344870, 62566960, 165866251, 63180877, 62356804, 64479173, 62098267, 64978197, 63123662] purine-containing compound metabolic process
GO:0072524 0.488 2.402 0.000e+00 2.903e-05 305 60 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 66137094, 5960044, 17046519, 17549174, 8200910, 65033516, 23090099, 30588025, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 3646533, 64427981, 4220178, 63649356, 62446788, 63517822, 62748898, 166499573, 62754658, 166165052, 63157973, 64380885, 65935692, 168089107, 63863560, 166574781, 62566960, 165866251, 64479173, 62098267, 64978197, 63123662] pyridine-containing compound metabolic process
GO:0006733 0.488 2.395 0.000e+00 2.750e-05 305 60 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 66137094, 5960044, 17046519, 17549174, 8200910, 65033516, 23090099, 30588025, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 3646533, 64427981, 4220178, 63649356, 62446788, 63517822, 62748898, 166499573, 62754658, 166165052, 63157973, 64380885, 65935692, 168089107, 63863560, 166574781, 62566960, 165866251, 64479173, 62098267, 64978197, 63123662] oxidoreduction coenzyme metabolic process
GO:0043043 0.437 2.372 0.000e+00 3.266e-05 377 94 [7655641, 64669875, 20323736, 33709212, 66453589, 67144272, 19107849, 29630217, 5141220, 8283720, 17035162, 60453073, 5645650, 28829095, 165941560, 3576806, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 40487328, 16968363, 38183434, 15916898, 5365520, 3492858, 41621220, 62224782, 10593880, 23449836, 36697039, 23721515, 38302786, 33208200, 12493950, 30459755, 31342205, 12690700, 67469358, 3497381, 62120168, 6962421, 51629989, 48778871, 65977279, 66402327, 68927583, 65259195, 21408386, 65777235, 20720618, 66350717, 66050469, 65886657, 66541818, 67061811, 168017014, 166807349, 7259645, 29341916, 67389484, 74406712, 82054302, 48590768, 167340047, 4774708, 166720030, 67911420, 64474525, 39007615, 42272589, 167990362, 66752541, 10899352, 167349682, 67383571, 65506212, 65977068, 65626218, 167623679, 38249992, 67911893, 67774188, 4009201, 166036375, 65669111, 10276368, 13581456] peptide biosynthetic process
GO:0006412 0.437 2.369 0.000e+00 3.110e-05 372 94 [7655641, 64669875, 20323736, 33709212, 66453589, 67144272, 19107849, 29630217, 5141220, 8283720, 17035162, 60453073, 5645650, 28829095, 165941560, 3576806, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 40487328, 16968363, 38183434, 15916898, 5365520, 3492858, 41621220, 62224782, 10593880, 23449836, 36697039, 23721515, 38302786, 33208200, 12493950, 30459755, 31342205, 12690700, 67469358, 3497381, 62120168, 6962421, 51629989, 48778871, 65977279, 66402327, 68927583, 65259195, 21408386, 65777235, 20720618, 66350717, 66050469, 65886657, 66541818, 67061811, 168017014, 166807349, 7259645, 29341916, 67389484, 74406712, 82054302, 48590768, 167340047, 4774708, 166720030, 67911420, 64474525, 39007615, 42272589, 167990362, 66752541, 10899352, 167349682, 67383571, 65506212, 65977068, 65626218, 167623679, 38249992, 67911893, 67774188, 4009201, 166036375, 65669111, 10276368, 13581456] translation
GO:0006518 0.437 2.362 0.000e+00 2.969e-05 378 94 [7655641, 64669875, 20323736, 33709212, 66453589, 67144272, 19107849, 29630217, 5141220, 8283720, 17035162, 60453073, 5645650, 28829095, 165941560, 3576806, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 40487328, 16968363, 38183434, 15916898, 5365520, 3492858, 41621220, 62224782, 10593880, 23449836, 36697039, 23721515, 38302786, 33208200, 12493950, 30459755, 31342205, 12690700, 67469358, 3497381, 62120168, 6962421, 51629989, 48778871, 65977279, 66402327, 68927583, 65259195, 21408386, 65777235, 20720618, 66350717, 66050469, 65886657, 66541818, 67061811, 168017014, 166807349, 7259645, 29341916, 67389484, 74406712, 82054302, 48590768, 167340047, 4774708, 166720030, 67911420, 64474525, 39007615, 42272589, 167990362, 66752541, 10899352, 167349682, 67383571, 65506212, 65977068, 65626218, 167623679, 38249992, 67911893, 67774188, 4009201, 166036375, 65669111, 10276368, 13581456] peptide metabolic process
GO:0043604 0.430 2.349 0.000e+00 2.840e-05 411 98 [7655641, 64669875, 20323736, 33709212, 66453589, 67144272, 19107849, 29630217, 5141220, 8283720, 17035162, 60453073, 5645650, 28829095, 165941560, 3576806, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 40487328, 16968363, 38183434, 15916898, 5365520, 3492858, 38111527, 41621220, 62224782, 10593880, 23449836, 36697039, 23721515, 38302786, 33208200, 12493950, 30459755, 31342205, 12690700, 67469358, 3497381, 62120168, 6962421, 51629989, 48778871, 65977279, 66402327, 68927583, 65259195, 21408386, 64164012, 65777235, 20720618, 66350717, 66050469, 62018486, 65886657, 66541818, 67061811, 168017014, 166807349, 7259645, 29341916, 67389484, 74406712, 82054302, 48590768, 167340047, 4774708, 166720030, 67911420, 64474525, 39007615, 42272589, 167990362, 66752541, 10899352, 167349682, 67383571, 65428360, 65506212, 65977068, 65626218, 167623679, 38249992, 67911893, 67774188, 4009201, 166036375, 65669111, 10276368, 13581456] amide biosynthetic process
GO:0043603 0.430 2.348 0.000e+00 2.722e-05 414 98 [7655641, 64669875, 20323736, 33709212, 66453589, 67144272, 19107849, 29630217, 5141220, 8283720, 17035162, 60453073, 5645650, 28829095, 165941560, 3576806, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 40487328, 16968363, 38183434, 15916898, 5365520, 3492858, 38111527, 41621220, 62224782, 10593880, 23449836, 36697039, 23721515, 38302786, 33208200, 12493950, 30459755, 31342205, 12690700, 67469358, 3497381, 62120168, 6962421, 51629989, 48778871, 65977279, 66402327, 68927583, 65259195, 21408386, 64164012, 65777235, 20720618, 66350717, 66050469, 62018486, 65886657, 66541818, 67061811, 168017014, 166807349, 7259645, 29341916, 67389484, 74406712, 82054302, 48590768, 167340047, 4774708, 166720030, 67911420, 64474525, 39007615, 42272589, 167990362, 66752541, 10899352, 167349682, 67383571, 65428360, 65506212, 65977068, 65626218, 167623679, 38249992, 67911893, 67774188, 4009201, 166036375, 65669111, 10276368, 13581456] cellular amide metabolic process
GO:0009056 0.459 2.344 0.000e+00 2.613e-05 409 70 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 4715355, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 61892960, 61635847, 67028544, 19508028, 59725586, 54913980, 30623941, 839701, 12964871, 21164095, 66137094, 5960044, 17046519, 17549174, 8200910, 65033516, 10631876, 23090099, 30588025, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 3646533, 61780119, 64427981, 4220178, 63649356, 62446788, 63517822, 62748898, 63332989, 166499573, 62754658, 166165052, 63157973, 64380885, 65935692, 168089107, 62566960, 165866251, 13604025, 62216988, 64479173, 13605039, 62098267, 64978197, 62450924, 63123662] catabolic process
GO:0016052 0.459 2.305 0.000e+00 3.517e-05 339 64 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 4715355, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 61635847, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 66137094, 5960044, 17046519, 17549174, 8200910, 65033516, 23090099, 30588025, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 3646533, 64427981, 4220178, 63649356, 62446788, 63517822, 62748898, 63332989, 166499573, 62754658, 166165052, 63157973, 64380885, 65935692, 168089107, 62566960, 165866251, 62216988, 64479173, 13605039, 62098267, 64978197, 62450924, 63123662] carbohydrate catabolic process
GO:0044712 0.455 2.296 0.000e+00 3.387e-05 355 67 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 4715355, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 61635847, 67028544, 19508028, 59725586, 54913980, 30623941, 839701, 12964871, 21164095, 66137094, 5960044, 17046519, 17549174, 8200910, 65033516, 23090099, 30588025, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 3646533, 64427981, 4220178, 63649356, 62446788, 63517822, 62748898, 63332989, 166499573, 62754658, 166165052, 63157973, 64380885, 65935692, 168089107, 62566960, 165866251, 13604025, 62216988, 64479173, 13605039, 62098267, 64978197, 62450924, 63123662] single-organism catabolic process
GO:0044724 0.459 2.293 0.000e+00 3.266e-05 336 64 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 4715355, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 61635847, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 66137094, 5960044, 17046519, 17549174, 8200910, 65033516, 23090099, 30588025, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 3646533, 64427981, 4220178, 63649356, 62446788, 63517822, 62748898, 63332989, 166499573, 62754658, 166165052, 63157973, 64380885, 65935692, 168089107, 62566960, 165866251, 62216988, 64479173, 13605039, 62098267, 64978197, 62450924, 63123662] single-organism carbohydrate catabolic process
GO:0043648 0.849 2.201 0.000e+00 1.126e-04 43 7 [13684061, 6155443, 11147909, 16967630, 21276719, 56134344, 16965587] dicarboxylic acid metabolic process
GO:0072350 0.785 2.145 3.589e-04 2.308e-04 29 8 [13684061, 78477008, 80889105, 26904631, 7496609, 20853009, 29983272, 3740901] tricarboxylic acid metabolic process
GO:0006732 0.416 2.118 0.000e+00 3.371e-04 391 71 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 67028544, 59725586, 54913980, 30623941, 38111527, 839701, 12964871, 66137094, 5960044, 17046519, 17549174, 8200910, 65033516, 23090099, 30588025, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 3646533, 64427981, 4220178, 63649356, 62446788, 63517822, 62748898, 64164012, 166499573, 62754658, 166165052, 63157973, 63603065, 64380885, 62018486, 65935692, 168089107, 45843396, 63863560, 166574781, 61901179, 63849179, 62479129, 65428360, 61880488, 42221176, 62566960, 165866251, 64479173, 62098267, 64978197, 63123662] coenzyme metabolic process
GO:0051186 0.410 2.111 0.000e+00 3.633e-04 413 72 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 67028544, 59725586, 54913980, 30623941, 38111527, 839701, 12964871, 66137094, 5960044, 17046519, 17549174, 8200910, 65033516, 23090099, 30588025, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 3646533, 64427981, 4220178, 63649356, 62446788, 63517822, 62748898, 64164012, 166499573, 62754658, 166165052, 63157973, 63603065, 64380885, 15754209, 62018486, 65935692, 168089107, 45843396, 63863560, 166574781, 61901179, 63849179, 62479129, 65428360, 61880488, 42221176, 62566960, 165866251, 64479173, 62098267, 64978197, 63123662] cofactor metabolic process
GO:0046364 0.627 1.969 1.775e-03 2.462e-03 107 12 [36454371, 839701, 12964871, 5960044, 17046519, 8200910, 65033516, 61982117, 61106614, 54789106, 49673151, 62446788] monosaccharide biosynthetic process
GO:0006091 0.371 1.943 1.526e-04 3.116e-03 474 79 [30875488, 17585926, 8107297, 14006785, 4543087, 4559493, 8170293, 4737261, 45207415, 29629717, 33420375, 9654148, 23089117, 25933508, 22187812, 63441836, 18275642, 67028544, 59725586, 54913980, 30623941, 839701, 12964871, 66137094, 5960044, 17046519, 17549174, 8200910, 65033516, 23090099, 30588025, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 3646533, 64427981, 4220178, 63649356, 62446788, 63517822, 13570629, 61600538, 62232545, 61963309, 61598826, 64109059, 62748898, 61600015, 62718684, 166499573, 59156012, 63039326, 62754658, 166165052, 63157973, 63112646, 64380885, 65657046, 57028376, 40551040, 65935692, 168089107, 61601993, 168109762, 62566960, 165866251, 167284707, 61621955, 64479173, 62098267, 64978197, 63123662, 61608244, 166278783] generation of precursor metabolites and energy
GO:1902578 0.466 1.792 8.900e-03 1.249e-02 132 23 [3885199, 1994037, 29978920, 33721585, 38210955, 54503535, 21357752, 32363526, 1809293, 268176, 21432496, 4416619, 29629513, 13568664, 65627086, 62354250, 165851092, 27807827, 62344870, 62156769, 165706474, 62660497, 67703402] single-organism localization
GO:0005996 0.396 1.696 1.375e-02 2.620e-02 222 34 [4715355, 80888632, 10226000, 30252792, 61635847, 8532970, 36454371, 839701, 12964871, 5960044, 17046519, 8200910, 65033516, 6997781, 61982117, 63371685, 17583418, 61106614, 54789106, 63640418, 49673151, 62952131, 62446788, 62209062, 62907054, 63167857, 62199335, 65811933, 67494413, 64328599, 63228299, 21899103, 63334059, 62216988] monosaccharide metabolic process
GO:0006414 0.571 1.679 2.109e-02 2.917e-02 74 10 [10185112, 8974409, 5730052, 4100571, 26879329, 61884939, 5753625, 30556349, 167619418, 29262834] translational elongation
GO:0015988 0.600 1.642 2.916e-02 3.675e-02 53 8 [1994037, 32363526, 1809293, 268176, 65627086, 62354250, 165851092, 62344870] energy coupled proton transmembrane transport, against electrochemical gradient
GO:0090662 0.600 1.632 2.964e-02 3.844e-02 53 8 [1994037, 32363526, 1809293, 268176, 65627086, 62354250, 165851092, 62344870] ATP hydrolysis coupled transmembrane transport
GO:0006457 0.615 1.614 3.307e-02 4.285e-02 47 7 [16968460, 7661714, 10924847, 21157792, 62273450, 64990955, 62089130] protein folding
GO:0015985 0.583 1.594 3.906e-02 4.792e-02 64 8 [1994037, 32363526, 1809293, 268176, 13568664, 65627086, 62354250, 62344870] energy coupled proton transport, down electrochemical gradient
GO:0009142 0.583 1.589 4.093e-02 4.827e-02 67 8 [1994037, 32363526, 1809293, 268176, 13568664, 65627086, 62354250, 62344870] nucleoside triphosphate biosynthetic process
GO:0006754 0.583 1.587 3.682e-02 4.777e-02 65 8 [1994037, 32363526, 1809293, 268176, 13568664, 65627086, 62354250, 62344870] ATP biosynthetic process
GO:0006006 0.446 1.566 3.943e-02 5.311e-02 135 17 [36454371, 839701, 12964871, 5960044, 17046519, 8200910, 65033516, 6997781, 61982117, 63371685, 61106614, 54789106, 63640418, 49673151, 62446788, 21899103, 62216988] glucose metabolic process
GO:0071702 0.472 1.564 4.102e-02 5.262e-02 54 14 [3885199, 29978920, 33721585, 38210955, 54503535, 21357752, 21432496, 4416619, 29629513, 27807827, 62156769, 165706474, 62660497, 67703402] organic substance transport

In [55]:
bp_rag


Out[55]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0006790 -0.670 -1.993 0.003 0.033 92 9 [63603065, 45843396, 61901179, 63849179, 65619550, 62479129, 61880488, 42221176, 20628827] sulfur compound metabolic process
GO:0022900 -0.617 -1.835 0.010 0.066 72 9 [61600538, 62232545, 61598826, 61600015, 61601993, 168109762, 61621955, 61608244, 166278783] electron transport chain
GO:0051234 -0.298 -1.762 0.003 0.075 331 88 [3885199, 1994037, 29978920, 33721585, 38210955, 54503535, 21357752, 32363526, 1809293, 268176, 21432496, 4416619, 29629513, 13568664, 63078357, 6924770, 63452797, 77351967, 10689069, 15207893, 28360306, 63332162, 17587826, 63205501, 32955361, 6347838, 31357673, 32157942, 13841186, 13203808, 62946388, 28669498, 61865720, 63129880, 65627086, 63468226, 63133221, 20629788, 63199719, 12378604, 40686252, 62354250, 168161151, 13571500, 65516796, 40674602, 28240379, 66978191, 63132923, 62545344, 167915219, 165851092, 28273397, 47513944, 63780068, 167285315, 13587543, 166593522, 167348034, 166208277, 27807827, 167156307, 62344870, 11992086, 10265600, 17618404, 56076521, 13570595, 13413281, 29505496, 22209574, 31262467, 33706145, 37969849, 63374013, 28423332, 166294804, 29374081, 165685567, 11412988, 62156769, 167645582, 165706474, 62660497, 167399046, 165992613, 167279298, 67703402] establishment of localization
GO:0051179 -0.298 -1.759 0.001 0.057 332 88 [3885199, 1994037, 29978920, 33721585, 38210955, 54503535, 21357752, 32363526, 1809293, 268176, 21432496, 4416619, 29629513, 13568664, 63078357, 6924770, 63452797, 77351967, 10689069, 15207893, 28360306, 63332162, 17587826, 63205501, 32955361, 6347838, 31357673, 32157942, 13841186, 13203808, 62946388, 28669498, 61865720, 63129880, 65627086, 63468226, 63133221, 20629788, 63199719, 12378604, 40686252, 62354250, 168161151, 13571500, 65516796, 40674602, 28240379, 66978191, 63132923, 62545344, 167915219, 165851092, 28273397, 47513944, 63780068, 167285315, 13587543, 166593522, 167348034, 166208277, 27807827, 167156307, 62344870, 11992086, 10265600, 17618404, 56076521, 13570595, 13413281, 29505496, 22209574, 31262467, 33706145, 37969849, 63374013, 28423332, 166294804, 29374081, 165685567, 11412988, 62156769, 167645582, 165706474, 62660497, 167399046, 165992613, 167279298, 67703402] localization
GO:0040011 -0.398 -1.679 0.020 0.077 274 24 [167307068, 13580518, 21419243, 48844574, 168130942, 166734854, 62626786, 11413856, 13586933, 22310619, 168062228, 167832826, 167438835, 44091081, 165775316, 166250719, 168173199, 165990924, 63837786, 168185530, 168106741, 167953213, 168192733, 167966912] locomotion

In [56]:
cc_rt


Out[56]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0044444 0.443 2.446 0.000e+00 0.000e+00 422 106 [7655641, 64669875, 20323736, 33709212, 66453589, 67144272, 29629717, 19107849, 29630217, 5141220, 8283720, 17035162, 23089117, 60453073, 5645650, 28829095, 165941560, 3576806, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 40487328, 16968363, 38183434, 15916898, 5365520, 80889105, 3492858, 41621220, 62224782, 10593880, 23449836, 36697039, 66137094, 23721515, 38302786, 33208200, 12493950, 30459755, 31342205, 17549174, 12690700, 67469358, 3497381, 6962421, 23090099, 65977279, 66402327, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 68927583, 62887295, 62783504, 65259195, 21408386, 65777235, 20720618, 66350717, 66050469, 65886657, 66541818, 67061811, 168017014, 166807349, 7259645, 29341916, 67389484, 74406712, 82054302, 48590768, 167340047, 4774708, 166720030, 67911420, 64474525, 39007615, 42272589, 167990362, 66752541, 10899352, 167349682, 67383571, 65506212, 65977068, 65626218, 62566960, 167623679, 38249992, 67911893, ...] cytoplasmic part
GO:1990904 0.446 2.397 0.000e+00 0.000e+00 360 91 [7655641, 64669875, 20323736, 33709212, 66453589, 67144272, 19107849, 29630217, 5141220, 8283720, 17035162, 60453073, 5645650, 28829095, 165941560, 3576806, 25902959, 20862748, 23226729, 6962424, 15891127, 29630113, 23720124, 6288540, 8107184, 20132923, 40487328, 16968363, 38183434, 15916898, 5365520, 3492858, 41621220, 62224782, 10593880, 23449836, 36697039, 23721515, 38302786, 33208200, 12493950, 30459755, 31342205, 12690700, 67469358, 3497381, 6962421, 65977279, 66402327, 68927583, 65259195, 21408386, 65777235, 20720618, 66350717, 66050469, 65886657, 66541818, 67061811, 168017014, 166807349, 7259645, 29341916, 67389484, 74406712, 82054302, 48590768, 167340047, 4774708, 166720030, 67911420, 64474525, 39007615, 42272589, 167990362, 66752541, 10899352, 167349682, 67383571, 65506212, 65977068, 65626218, 167623679, 38249992, 67911893, 67774188, 4009201, 166036375, 65669111, 10276368, 13581456] ribonucleoprotein complex
GO:0005840 0.427 2.263 0.000e+00 1.113e-04 319 82 [7655641, 64669875, 20323736, 33709212, 66453589, 67144272, 19107849, 29630217, 5141220, 60453073, 5645650, 28829095, 165941560, 3576806, 25902959, 20862748, 15891127, 29630113, 23720124, 8107184, 40487328, 16968363, 38183434, 15916898, 5365520, 3492858, 41621220, 62224782, 10593880, 23449836, 36697039, 23721515, 38302786, 33208200, 12493950, 30459755, 31342205, 12690700, 67469358, 3497381, 6962421, 65977279, 68927583, 21408386, 65777235, 20720618, 66350717, 66050469, 65886657, 66541818, 67061811, 168017014, 166807349, 7259645, 29341916, 67389484, 74406712, 82054302, 48590768, 167340047, 4774708, 166720030, 67911420, 64474525, 39007615, 42272589, 167990362, 66752541, 10899352, 167349682, 67383571, 65506212, 65977068, 65626218, 167623679, 38249992, 67911893, 67774188, 4009201, 166036375, 10276368, 13581456] ribosome
GO:0043229 0.427 2.256 0.000e+00 1.043e-04 327 82 [7655641, 64669875, 20323736, 33709212, 66453589, 67144272, 19107849, 29630217, 5141220, 60453073, 5645650, 28829095, 165941560, 3576806, 25902959, 20862748, 15891127, 29630113, 23720124, 8107184, 40487328, 16968363, 38183434, 15916898, 5365520, 3492858, 41621220, 62224782, 10593880, 23449836, 36697039, 23721515, 38302786, 33208200, 12493950, 30459755, 31342205, 12690700, 67469358, 3497381, 6962421, 65977279, 68927583, 21408386, 65777235, 20720618, 66350717, 66050469, 65886657, 66541818, 67061811, 168017014, 166807349, 7259645, 29341916, 67389484, 74406712, 82054302, 48590768, 167340047, 4774708, 166720030, 67911420, 64474525, 39007615, 42272589, 167990362, 66752541, 10899352, 167349682, 67383571, 65506212, 65977068, 65626218, 167623679, 38249992, 67911893, 67774188, 4009201, 166036375, 10276368, 13581456] intracellular organelle
GO:0043232 0.427 2.250 0.000e+00 1.002e-04 320 82 [7655641, 64669875, 20323736, 33709212, 66453589, 67144272, 19107849, 29630217, 5141220, 60453073, 5645650, 28829095, 165941560, 3576806, 25902959, 20862748, 15891127, 29630113, 23720124, 8107184, 40487328, 16968363, 38183434, 15916898, 5365520, 3492858, 41621220, 62224782, 10593880, 23449836, 36697039, 23721515, 38302786, 33208200, 12493950, 30459755, 31342205, 12690700, 67469358, 3497381, 6962421, 65977279, 68927583, 21408386, 65777235, 20720618, 66350717, 66050469, 65886657, 66541818, 67061811, 168017014, 166807349, 7259645, 29341916, 67389484, 74406712, 82054302, 48590768, 167340047, 4774708, 166720030, 67911420, 64474525, 39007615, 42272589, 167990362, 66752541, 10899352, 167349682, 67383571, 65506212, 65977068, 65626218, 167623679, 38249992, 67911893, 67774188, 4009201, 166036375, 10276368, 13581456] intracellular non-membrane-bounded organelle
GO:0044445 0.645 2.130 7.000e-04 3.895e-04 47 14 [29629717, 23089117, 66137094, 17549174, 23090099, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 62566960] cytosolic part
GO:0000015 0.645 2.126 5.268e-04 3.458e-04 43 14 [29629717, 23089117, 66137094, 17549174, 23090099, 66797374, 62848403, 31709972, 20853105, 18120033, 22213675, 62887295, 62783504, 62566960] phosphopyruvate hydratase complex
GO:0015934 0.691 2.105 5.253e-04 3.651e-04 63 11 [7655641, 64669875, 20323736, 33709212, 8283720, 17035162, 15891127, 41621220, 21408386, 10899352, 38249992] large ribosomal subunit
GO:0005737 0.412 1.901 1.276e-03 2.764e-03 264 47 [4715355, 1488186, 22444626, 80888632, 33721585, 78477008, 167451486, 7618450, 21157792, 10226000, 62309035, 30252792, 61635847, 8532970, 19508028, 28314259, 21164095, 167938999, 13569694, 12905190, 62120168, 51629989, 48778871, 7013360, 17583418, 62273450, 28437551, 62209062, 62907054, 63167857, 62199335, 64990955, 65811933, 62322368, 67494413, 61615972, 63648739, 63662802, 27807827, 51262100, 62316849, 12417159, 22244214, 167277486, 165706474, 63180877, 62216988] cytoplasm
GO:0005622 0.368 1.846 7.762e-04 4.298e-03 306 64 [7655641, 64669875, 20323736, 33709212, 19107849, 29630217, 5141220, 10185112, 60453073, 5645650, 28829095, 165941560, 3576806, 25902959, 20862748, 8974409, 5730052, 15891127, 4100571, 26879329, 41621220, 23449836, 3884277, 61884939, 67469358, 3497381, 6962421, 65977279, 5753625, 30556349, 65259195, 21408386, 167619418, 20720618, 66350717, 66050469, 44091081, 63035046, 65886657, 66541818, 67061811, 168017014, 166807349, 7259645, 29341916, 67389484, 74406712, 82054302, 48590768, 167340047, 4774708, 64474525, 42272589, 45593936, 10899352, 165990924, 63837786, 67383571, 29262834, 38249992, 67774188, 65669111, 13604374, 10276368] intracellular
GO:0044446 0.396 1.754 7.877e-03 8.794e-03 169 38 [7655641, 64669875, 20323736, 33709212, 8283720, 17035162, 23226729, 6962424, 15891127, 6288540, 20132923, 3492858, 41621220, 10593880, 66402327, 68927583, 65259195, 21408386, 20720618, 66350717, 66050469, 65886657, 66541818, 67061811, 168017014, 166807349, 7259645, 29341916, 67389484, 74406712, 82054302, 48590768, 167340047, 4774708, 166720030, 10899352, 38249992, 65669111] intracellular organelle part
GO:0044391 0.396 1.730 1.018e-02 9.765e-03 159 38 [7655641, 64669875, 20323736, 33709212, 8283720, 17035162, 23226729, 6962424, 15891127, 6288540, 20132923, 3492858, 41621220, 10593880, 66402327, 68927583, 65259195, 21408386, 20720618, 66350717, 66050469, 65886657, 66541818, 67061811, 168017014, 166807349, 7259645, 29341916, 67389484, 74406712, 82054302, 48590768, 167340047, 4774708, 166720030, 10899352, 38249992, 65669111] ribosomal subunit

In [57]:
cc_rag


Out[57]:
es nes pval fdr gene_set_size matched_size genes name
Term
GO:0043190 -0.570 -2.912 0.000e+00 0.000 115 47 [63078357, 6924770, 63452797, 77351967, 10689069, 15207893, 28360306, 63332162, 17587826, 63205501, 32955361, 6347838, 31357673, 32157942, 13841186, 13203808, 62946388, 28669498, 61865720, 63129880, 63468226, 63133221, 20629788, 63199719, 12378604, 40686252, 168161151, 65516796, 40674602, 28240379, 66978191, 63132923, 62545344, 167915219, 28273397, 47513944, 11992086, 10265600, 17618404, 56076521, 13413281, 29505496, 22209574, 31262467, 33706145, 37969849, 63374013] ATP-binding cassette (ABC) transporter complex
GO:1990351 -0.570 -2.910 0.000e+00 0.000 117 47 [63078357, 6924770, 63452797, 77351967, 10689069, 15207893, 28360306, 63332162, 17587826, 63205501, 32955361, 6347838, 31357673, 32157942, 13841186, 13203808, 62946388, 28669498, 61865720, 63129880, 63468226, 63133221, 20629788, 63199719, 12378604, 40686252, 168161151, 65516796, 40674602, 28240379, 66978191, 63132923, 62545344, 167915219, 28273397, 47513944, 11992086, 10265600, 17618404, 56076521, 13413281, 29505496, 22209574, 31262467, 33706145, 37969849, 63374013] transporter complex
GO:0098797 -0.570 -2.900 0.000e+00 0.000 117 47 [63078357, 6924770, 63452797, 77351967, 10689069, 15207893, 28360306, 63332162, 17587826, 63205501, 32955361, 6347838, 31357673, 32157942, 13841186, 13203808, 62946388, 28669498, 61865720, 63129880, 63468226, 63133221, 20629788, 63199719, 12378604, 40686252, 168161151, 65516796, 40674602, 28240379, 66978191, 63132923, 62545344, 167915219, 28273397, 47513944, 11992086, 10265600, 17618404, 56076521, 13413281, 29505496, 22209574, 31262467, 33706145, 37969849, 63374013] plasma membrane protein complex
GO:1904949 -0.570 -2.891 0.000e+00 0.000 117 47 [63078357, 6924770, 63452797, 77351967, 10689069, 15207893, 28360306, 63332162, 17587826, 63205501, 32955361, 6347838, 31357673, 32157942, 13841186, 13203808, 62946388, 28669498, 61865720, 63129880, 63468226, 63133221, 20629788, 63199719, 12378604, 40686252, 168161151, 65516796, 40674602, 28240379, 66978191, 63132923, 62545344, 167915219, 28273397, 47513944, 11992086, 10265600, 17618404, 56076521, 13413281, 29505496, 22209574, 31262467, 33706145, 37969849, 63374013] ATPase complex
GO:0044459 -0.570 -2.890 0.000e+00 0.000 119 47 [63078357, 6924770, 63452797, 77351967, 10689069, 15207893, 28360306, 63332162, 17587826, 63205501, 32955361, 6347838, 31357673, 32157942, 13841186, 13203808, 62946388, 28669498, 61865720, 63129880, 63468226, 63133221, 20629788, 63199719, 12378604, 40686252, 168161151, 65516796, 40674602, 28240379, 66978191, 63132923, 62545344, 167915219, 28273397, 47513944, 11992086, 10265600, 17618404, 56076521, 13413281, 29505496, 22209574, 31262467, 33706145, 37969849, 63374013] plasma membrane part
GO:0098796 -0.366 -1.959 5.537e-04 0.004 171 56 [1994037, 32363526, 1809293, 268176, 13568664, 63078357, 6924770, 63452797, 77351967, 10689069, 15207893, 28360306, 63332162, 17587826, 63205501, 32955361, 6347838, 31357673, 32157942, 13841186, 13203808, 62946388, 28669498, 61865720, 63129880, 65627086, 63468226, 63133221, 20629788, 63199719, 12378604, 40686252, 62354250, 168161151, 65516796, 40674602, 28240379, 66978191, 63132923, 62545344, 167915219, 165851092, 28273397, 47513944, 62344870, 11992086, 10265600, 17618404, 56076521, 13413281, 29505496, 22209574, 31262467, 33706145, 37969849, 63374013] membrane protein complex
GO:0043234 -0.366 -1.952 1.405e-03 0.003 180 56 [1994037, 32363526, 1809293, 268176, 13568664, 63078357, 6924770, 63452797, 77351967, 10689069, 15207893, 28360306, 63332162, 17587826, 63205501, 32955361, 6347838, 31357673, 32157942, 13841186, 13203808, 62946388, 28669498, 61865720, 63129880, 65627086, 63468226, 63133221, 20629788, 63199719, 12378604, 40686252, 62354250, 168161151, 65516796, 40674602, 28240379, 66978191, 63132923, 62545344, 167915219, 165851092, 28273397, 47513944, 62344870, 11992086, 10265600, 17618404, 56076521, 13413281, 29505496, 22209574, 31262467, 33706145, 37969849, 63374013] protein complex
GO:0016020 -0.551 -1.887 6.812e-03 0.005 75 13 [21357752, 21687303, 63780068, 166593522, 167156307, 62830069, 165685567, 166216926, 166632550, 62660497, 61957888, 27635679, 167701862] membrane
GO:0044425 -0.332 -1.818 1.959e-03 0.008 191 62 [1994037, 33721585, 21687303, 32363526, 1809293, 268176, 13568664, 63078357, 6924770, 63452797, 77351967, 10689069, 15207893, 28360306, 63332162, 17587826, 63205501, 32955361, 6347838, 31357673, 32157942, 13841186, 13203808, 62946388, 28669498, 61865720, 63129880, 65627086, 63468226, 63133221, 20629788, 63199719, 12378604, 40686252, 62354250, 168161151, 65516796, 40674602, 28240379, 66978191, 63132923, 62545344, 167915219, 165851092, 28273397, 47513944, 27807827, 62344870, 11992086, 10265600, 17618404, 56076521, 13413281, 29505496, 22209574, 31262467, 33706145, 37969849, 63374013, 62830069, 165706474, 67703402] membrane part