gsea algorithm: http://software.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.html
gseapy: https://media.readthedocs.org/pdf/gseapy/latest/gseapy.pdf
https://github.com/stuppie/CM7_CM1E2d56col_unenr123_rawextract_2017/blob/master/scripts/gseapy.ipynb
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
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
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
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
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
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
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
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
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
Content source: stuppie/CM7_CM1E2d56col_unenr123_rawextract_2017
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