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import NotebookImport
from metaPCNA import *
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import GTEX as GTEX
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f_win.order().tail()
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gabr = [g for g in rna_df.index if g.startswith('GABR')]
f = dx_rna.ix[gabr].dropna()
f.join(f_win).sort(f_win.name)
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GTEX.plot_tissues_across_gene('GABRD', log=True)
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gtex = np.log2(GTEX.gtex)
meta = GTEX.meta
tissue_type = GTEX.tissue_type
GABRD is highly expressed in many areas of the brain as well as in the testis. Interestingly it is the highest expressed subunit in the testis.
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mm = gtex.ix[gabr].dropna().T.groupby(meta['SMTSD']).median()
mm = mm.clip_lower(-10)
mm.rank(1, ascending=False)['GABRD'].order().head(10)
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Here I'm plotting the different GABA receptors expression distribution in Testes.
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fig, ax = subplots(figsize=(10,4))
o = ['GABRA1','GABRA2', 'GABRA3', 'GABRA4', 'GABRA5',
'GABRB1', 'GABRB2', 'GABRB3',
'GABRR1', 'GABRR2', 'GABRR3',
'GABRD','GABRE','GABRP','GABRQ']
c = sns.color_palette('muted', n_colors=7, desat=.7)
dd = gtex.ix[o, ti(tissue_type == 'Testis')].dropna(1)
sns.violinplot(dd.clip_lower(-4.).T, order=o,
names=[s[4:] for s in o],
inner='points', alpha=.7,
color=[c[0]]*5 + [c[1]]*3 + [c[2]]*3 + c[3:])
ax.set_xlabel('GABA subunit')
ax.set_ylabel('GTEX- Testis Expression (Log2)')
prettify_ax(ax)
fig.savefig(FIGDIR + 'Fig_S6.pdf')
There is a correlation of subunit expression in the testis with fraction upregulated in cancer across the GABA subunits.
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series_scatter(dx_rna.frac.ix[gabr],
gtex.ix[gabr].dropna().T.groupby(meta['SMTSD']).median().ix['Testis'])
In the testis
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sns.clustermap(gtex.ix[gabr, ti(meta['SMTSD'] == 'Testis')].T.corr())
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In the cerebellum
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bella = ti(meta['SMTSD'].dropna().str.contains('Cerebellum'))
sns.clustermap(gtex.ix[gabr, bella].T.corr())
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For TCGA differential expression
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sns.clustermap(dx.ix[gabr].T.corr().clip(-.5,.5))
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