analysis/GRO_seq_TFSEE/closest_genes.py

+import pandas as pd
+import numpy as np
+import csv
+import matplotlib.pyplot as plt
+import seaborn as sns
+import scipy
+
+# Find nearest genes
+
+# Grab TF FPKM levels
+fpkm = pd.read_table("rna.tsv")
+gene_names_mapping = pd.read_csv("../gencode.v19.annotation_protein_coding_ids.txt",names=['gene_id', 'symbol'])
+fpkm_symbol = fpkm.merge(gene_names_mapping)
+fpkm_symbol = fpkm.set_index(['gene_id'])
+
+# Enhancers
+enhancers_universe = pd.DataFrame.from_csv("GRO-seq_enhancers.bed", sep="\t", header=None, index_col=3)
+
+
+# Read in cluster 4 enhancers
+cluster_4 = pd.DataFrame.from_csv("cluster_4_enhancers.csv", sep=",", header=0, index_col=0)
+
+# Choose enhacners exprssed in cluster 4
+enhancers_universe_cluster_4 = enhancers_universe.loc[cluster_4.index.values]
+enhancers_universe_cluster_4.to_csv("cluster_4_enhancers_locations.bed", sep="\t",header=None, index=False)
+
+
+# Read in nearest genes
+genes_id = pd.DataFrame.from_csv("cluster_4_genes.txt", sep="\t", header=None, index_col=None)
+
+needed_rows = [row for row in fpkm_symbol.index if row in genes_id[0].values]
+cluster4_genes_expressed = fpkm_symbol.loc[needed_rows]
+
+
+# col_colors
+plt.style.use('classic')
+colors = ["#FFD66F","#2E6A44","#862743", "#4FA6C7", "#3398CC"]
+medianprops = dict(linestyle='-', linewidth=2, color='black')
+box = cluster4_genes_expressed.boxplot(column=['ES_D0', 'ES_D2', 'ES_D5', 'ES_D7',  'ES_D10'],patch_artist=True,showfliers=False,manage_xticks=False,widths = 0.6, medianprops = medianprops)
+plt.setp(box['whiskers'], color='k', linestyle='-', linewidth = 5)
+plt.setp(box['boxes'], color='k', linestyle='-', linewidth = 5)
+
+for patch, color in zip(box['boxes'], colors):
+    patch.set_facecolor(color)
+
+plt.tick_params(axis='y', direction='out')
+plt.tick_params(axis='x', direction='out')
+plt.tick_params(top='off', right='off')
+plt.grid(b=False)
+plt.ylim((-5,60))
+plt.xticks([1,2,3,4,5], ['ES_D0', 'ES_D2', 'ES_D5', 'ES_D7',  'ES_D10'])
+plt.savefig('box_plot_cluster_4_genes_fpkm.png')
+plt.clf()
+
+# Cluster tfs 0.05
+scipy.stats.ranksums(cluster4_genes_expressed['ES_D0'],cluster4_genes_expressed['ES_D2'])
+scipy.stats.ranksums(cluster4_genes_expressed['ES_D0'],cluster4_genes_expressed['ES_D5'])
+scipy.stats.ranksums(cluster4_genes_expressed['ES_D0'],cluster4_genes_expressed['ES_D7'])
+scipy.stats.ranksums(cluster4_genes_expressed['ES_D0'],cluster4_genes_expressed['ES_D10'])
+
+
+scipy.stats.ranksums(cluster4_genes_expressed['ES_D2'],cluster4_genes_expressed['ES_D5'])
+scipy.stats.ranksums(cluster4_genes_expressed['ES_D2'],cluster4_genes_expressed['ES_D7'])
+scipy.stats.ranksums(cluster4_genes_expressed['ES_D2'],cluster4_genes_expressed['ES_D10'])
+
+scipy.stats.ranksums(cluster4_genes_expressed['ES_D5'],cluster4_genes_expressed['ES_D7'])
+scipy.stats.ranksums(cluster4_genes_expressed['ES_D5'],cluster4_genes_expressed['ES_D10'])
+
+scipy.stats.ranksums(cluster4_genes_expressed['ES_D7'],cluster4_genes_expressed['ES_D10'])
+
+
+# Read in cluster 3 enhancers
+cluster_3 = pd.DataFrame.from_csv("cluster_3_enhancers.csv", sep=",", header=0, index_col=0)
+
+# Choose enhacners exprssed in cluster 3
+enhancers_universe_cluster_3 = enhancers_universe.loc[cluster_3.index.values]
+enhancers_universe_cluster_3.to_csv("cluster_3_enhancers_locations.bed", sep="\t",header=None, index=False)
+
+
+# Read in nearest genes
+genes_id = pd.DataFrame.from_csv("cluster_3_genes.txt", sep="\t", header=None, index_col=None)
+
+needed_rows = [row for row in fpkm_symbol.index if row in genes_id[0].values]
+cluster3_genes_expressed = fpkm_symbol.loc[needed_rows]
+
+
+# col_colors
+plt.style.use('classic')
+colors = ["#FFD66F","#2E6A44","#862743", "#4FA6C7", "#3398CC"]
+medianprops = dict(linestyle='-', linewidth=2, color='black')
+box = cluster3_genes_expressed.boxplot(column=['ES_D0', 'ES_D2', 'ES_D5', 'ES_D7',  'ES_D10'],patch_artist=True,showfliers=False,manage_xticks=False,widths = 0.6, medianprops = medianprops)
+plt.setp(box['whiskers'], color='k', linestyle='-', linewidth = 5)
+plt.setp(box['boxes'], color='k', linestyle='-', linewidth = 5)
+
+for patch, color in zip(box['boxes'], colors):
+    patch.set_facecolor(color)
+
+plt.tick_params(axis='y', direction='out')
+plt.tick_params(axis='x', direction='out')
+plt.tick_params(top='off', right='off')
+plt.grid(b=False)
+plt.ylim((-5,50))
+plt.xticks([1,2,3,4,5], ['ES_D0', 'ES_D2', 'ES_D5', 'ES_D7',  'ES_D10'])
+plt.savefig('box_plot_cluster_3_genes_fpkm.png')
+plt.clf()
+
+# Cluster tfs 1 e-4
+scipy.stats.ranksums(cluster3_genes_expressed['ES_D0'],cluster3_genes_expressed['ES_D2'])
+scipy.stats.ranksums(cluster3_genes_expressed['ES_D0'],cluster3_genes_expressed['ES_D5'])
+scipy.stats.ranksums(cluster3_genes_expressed['ES_D0'],cluster3_genes_expressed['ES_D7'])
+scipy.stats.ranksums(cluster3_genes_expressed['ES_D0'],cluster3_genes_expressed['ES_D10'])
+
+
+scipy.stats.ranksums(cluster3_genes_expressed['ES_D2'],cluster3_genes_expressed['ES_D5'])
+scipy.stats.ranksums(cluster3_genes_expressed['ES_D2'],cluster3_genes_expressed['ES_D7'])
+scipy.stats.ranksums(cluster3_genes_expressed['ES_D2'],cluster3_genes_expressed['ES_D10'])
+
+scipy.stats.ranksums(cluster3_genes_expressed['ES_D5'],cluster3_genes_expressed['ES_D7'])
+scipy.stats.ranksums(cluster3_genes_expressed['ES_D5'],cluster3_genes_expressed['ES_D10'])
+
+scipy.stats.ranksums(cluster3_genes_expressed['ES_D7'],cluster3_genes_expressed['ES_D10'])
+
+
+
+# Read in cluster 1 enhancers
+cluster_1 = pd.DataFrame.from_csv("cluster_1_enhancers.csv", sep=",", header=0, index_col=0)
+
+# Choose enhacners exprssed in cluster 1
+enhancers_universe_cluster_1 = enhancers_universe.loc[cluster_1.index.values]
+enhancers_universe_cluster_1.to_csv("cluster_1_enhancers_locations.bed", sep="\t",header=None, index=False)
+
+
+# Read in nearest genes
+genes_id = pd.DataFrame.from_csv("cluster_1_genes.txt", sep="\t", header=None, index_col=None)
+
+needed_rows = [row for row in fpkm_symbol.index if row in genes_id[0].values]
+cluster1_genes_expressed = fpkm_symbol.loc[needed_rows]
+
+
+# col_colors
+plt.style.use('classic')
+colors = ["#FFD66F","#2E6A44","#862743", "#4FA6C7", "#3398CC"]
+medianprops = dict(linestyle='-', linewidth=2, color='black')
+box = cluster1_genes_expressed.boxplot(column=['ES_D0', 'ES_D2', 'ES_D5', 'ES_D7',  'ES_D10'],patch_artist=True,showfliers=False,manage_xticks=False,widths = 0.6, medianprops = medianprops)
+plt.setp(box['whiskers'], color='k', linestyle='-', linewidth = 5)
+plt.setp(box['boxes'], color='k', linestyle='-', linewidth = 5)
+
+for patch, color in zip(box['boxes'], colors):
+    patch.set_facecolor(color)
+
+plt.tick_params(axis='y', direction='out')
+plt.tick_params(axis='x', direction='out')
+plt.tick_params(top='off', right='off')
+plt.grid(b=False)
+plt.ylim((-5,55))
+plt.xticks([1,2,3,4,5], ['ES_D0', 'ES_D2', 'ES_D5', 'ES_D7',  'ES_D10'])
+plt.savefig('box_plot_cluster_1_genes_fpkm.png')
+plt.clf()
+
+# Cluster tfs 1 e-4
+scipy.stats.ranksums(cluster1_genes_expressed['ES_D0'],cluster1_genes_expressed['ES_D2'])
+scipy.stats.ranksums(cluster1_genes_expressed['ES_D0'],cluster1_genes_expressed['ES_D5'])
+scipy.stats.ranksums(cluster1_genes_expressed['ES_D0'],cluster1_genes_expressed['ES_D7'])
+scipy.stats.ranksums(cluster1_genes_expressed['ES_D0'],cluster1_genes_expressed['ES_D10'])
+
+
+scipy.stats.ranksums(cluster1_genes_expressed['ES_D2'],cluster1_genes_expressed['ES_D5'])
+scipy.stats.ranksums(cluster1_genes_expressed['ES_D2'],cluster1_genes_expressed['ES_D7'])
+scipy.stats.ranksums(cluster1_genes_expressed['ES_D2'],cluster1_genes_expressed['ES_D10'])
+
+scipy.stats.ranksums(cluster1_genes_expressed['ES_D5'],cluster1_genes_expressed['ES_D7'])
+scipy.stats.ranksums(cluster1_genes_expressed['ES_D5'],cluster1_genes_expressed['ES_D10'])
+
+scipy.stats.ranksums(cluster1_genes_expressed['ES_D7'],cluster1_genes_expressed['ES_D10'])
+
+
+# Read in cluster 2 enhancers
+cluster_2 = pd.DataFrame.from_csv("cluster_2_enhancers.csv", sep=",", header=0, index_col=0)
+
+# Choose enhacners exprssed in cluster 2
+enhancers_universe_cluster_2 = enhancers_universe.loc[cluster_2.index.values]
+enhancers_universe_cluster_2.to_csv("cluster_2_enhancers_locations.bed", sep="\t",header=None, index=False)
+
+
+# Read in nearest genes
+genes_id = pd.DataFrame.from_csv("cluster_2_genes.txt", sep="\t", header=None, index_col=None)
+
+needed_rows = [row for row in fpkm_symbol.index if row in genes_id[0].values]
+cluster2_genes_expressed = fpkm_symbol.loc[needed_rows]
+
+
+# col_colors
+plt.style.use('classic')
+colors = ["#FFD66F","#2E6A44","#862743", "#4FA6C7", "#3398CC"]
+medianprops = dict(linestyle='-', linewidth=2, color='black')
+box = cluster2_genes_expressed.boxplot(column=['ES_D0', 'ES_D2', 'ES_D5', 'ES_D7',  'ES_D10'],patch_artist=True,showfliers=False,manage_xticks=False,widths = 0.6, medianprops = medianprops)
+plt.setp(box['whiskers'], color='k', linestyle='-', linewidth = 5)
+plt.setp(box['boxes'], color='k', linestyle='-', linewidth = 5)
+
+for patch, color in zip(box['boxes'], colors):
+    patch.set_facecolor(color)
+
+plt.tick_params(axis='y', direction='out')
+plt.tick_params(axis='x', direction='out')
+plt.tick_params(top='off', right='off')
+plt.grid(b=False)
+plt.ylim((-5,50))
+plt.xticks([1,2,3,4,5], ['ES_D0', 'ES_D2', 'ES_D5', 'ES_D7',  'ES_D10'])
+plt.savefig('box_plot_cluster_2_genes_fpkm.png')
+plt.clf()
+
+# Cluster tfs 1 e-4
+scipy.stats.ranksums(cluster2_genes_expressed['ES_D0'],cluster2_genes_expressed['ES_D2'])
+scipy.stats.ranksums(cluster2_genes_expressed['ES_D0'],cluster2_genes_expressed['ES_D5'])
+scipy.stats.ranksums(cluster2_genes_expressed['ES_D0'],cluster2_genes_expressed['ES_D7'])
+scipy.stats.ranksums(cluster2_genes_expressed['ES_D0'],cluster2_genes_expressed['ES_D10'])
+
+
+scipy.stats.ranksums(cluster2_genes_expressed['ES_D2'],cluster2_genes_expressed['ES_D5'])
+scipy.stats.ranksums(cluster2_genes_expressed['ES_D2'],cluster2_genes_expressed['ES_D7'])
+scipy.stats.ranksums(cluster2_genes_expressed['ES_D2'],cluster2_genes_expressed['ES_D10'])
+
+scipy.stats.ranksums(cluster2_genes_expressed['ES_D5'],cluster2_genes_expressed['ES_D7'])
+scipy.stats.ranksums(cluster2_genes_expressed['ES_D5'],cluster2_genes_expressed['ES_D10'])
+
+scipy.stats.ranksums(cluster2_genes_expressed['ES_D7'],cluster2_genes_expressed['ES_D10'])

analysis/GRO_seq_TFSEE/closest_genes.sh

+#Closest genes Cluster 4
+bedtools sort -i cluster_4_enhancers_locations.bed | bedtools closest -a - -b  gencode.v19.annotation_protein_coding_sorted.gtf | cut -f12 | cut -f1 -d ';' | cut -f2 -d ' ' | sort | uniq | sed 's/"//g' > cluster_4_genes.txt
+
+
+#Closest genes Cluster 3
+bedtools sort -i cluster_3_enhancers_locations.bed | bedtools closest -a - -b  gencode.v19.annotation_protein_coding_sorted.gtf | cut -f12 | cut -f1 -d ';' | cut -f2 -d ' ' | sort | uniq | sed 's/"//g' > cluster_3_genes.txt
+
+
+#Closest genes Cluster 1
+bedtools sort -i cluster_1_enhancers_locations.bed | bedtools closest -a - -b  gencode.v19.annotation_protein_coding_sorted.gtf | cut -f12 | cut -f1 -d ';' | cut -f2 -d ' ' | sort | uniq | sed 's/"//g' > cluster_1_genes.txt
+
+
+#Closest genes Cluster 2
+bedtools sort -i cluster_2_enhancers_locations.bed | bedtools closest -a - -b  gencode.v19.annotation_protein_coding_sorted.gtf | cut -f12 | cut -f1 -d ';' | cut -f2 -d ' ' | sort | uniq | sed 's/"//g' > cluster_2_genes.txt

analysis/GRO_seq_TFSEE/cluster1_enriched_tfs.csv

+,Unnamed: 0,ES_D0,ES_D2,ES_D5,ES_D7,ES_D10,cluster,early,late,diff,rank
+0,AR,0.572016047597,-0.8206442490639999,-0.282479909509,-0.5994848971010001,-0.561286507377,0,-0.35234990148625,-0.282479909509,-0.06986999197725002,15.0
+5,CEBPB,0.210109225919,-0.127176936493,-0.5803963676730001,-0.826459696747,-0.750630557991,0,-0.373539491328,-0.5803963676730001,0.20685687634500005,38.0
+6,CEBPD,0.210545644703,0.00987813393573,-0.955346518514,-0.826459696747,-0.49980984465899997,0,-0.2764614406918175,-0.955346518514,0.6788850778221824,53.0
+7,CEBPE,-0.831203544052,-0.8206442490639999,-0.955346518514,-0.826459696747,-0.763419237407,0,-0.8104316818175,-0.955346518514,0.14491483669649996,27.0
+8,CEBPG,0.0902638363663,0.0788920091117,-0.18159976155000002,-0.527987724308,-0.763419237407,0,-0.28056277905925,-0.18159976155000002,-0.09896301750924996,12.0
+14,DDIT3,-0.831203544052,0.779148451969,-0.356059344411,0.378473791618,-0.578266152953,0,-0.06296186335450002,-0.356059344411,0.2930974810565,43.0
+20,EGR2,-0.831203544052,-0.8206442490639999,-0.955346518514,0.951339729967,-0.763419237407,0,-0.365981825139,-0.955346518514,0.589364693375,51.0
+21,EGR3,-0.831203544052,-0.8206442490639999,-0.955346518514,0.048029995605699996,-0.24971279242400002,0,-0.46338264748357505,-0.955346518514,0.49196387103042494,47.0
+22,EGR4,-0.831203544052,-0.8206442490639999,-0.955346518514,0.049451275209699996,-0.763419237407,0,-0.591453938828325,-0.955346518514,0.363892579685675,45.0
+25,ELF3,-0.831203544052,-0.638711161513,-0.8424767248109999,0.7503665304420001,-0.08961497138329999,0,-0.20229078662657496,-0.8424767248109999,0.6401859381844249,52.0
+29,ESR1,-0.831203544052,-0.8206442490639999,-0.955346518514,-0.826459696747,-0.763419237407,0,-0.8104316818175,-0.955346518514,0.14491483669649996,27.0
+30,ESR2,-0.831203544052,-0.8206442490639999,-0.955346518514,-0.7342568702850001,0.738125636296,0,-0.4119947567762501,-0.955346518514,0.5433517617377499,49.0
+31,FIGLA,-0.831203544052,-0.8206442490639999,-0.955346518514,-0.826459696747,-0.763419237407,0,-0.8104316818175,-0.955346518514,0.14491483669649996,27.0
+33,FOSL2,-0.430224618332,-0.8206442490639999,-0.906897453893,0.956915779117,0.10390867019,0,-0.047511104522250006,-0.906897453893,0.85938634937075,60.0
+34,FOXC2,-0.831203544052,-0.8206442490639999,-0.955346518514,-0.826459696747,-0.763419237407,0,-0.8104316818175,-0.955346518514,0.14491483669649996,27.0
+40,GCM2,-0.831203544052,-0.8206442490639999,-0.955346518514,-0.826459696747,-0.763419237407,0,-0.8104316818175,-0.955346518514,0.14491483669649996,27.0
+41,GFI1B,-0.831203544052,-0.8206442490639999,-0.955346518514,-0.826459696747,-0.763419237407,0,-0.8104316818175,-0.955346518514,0.14491483669649996,27.0
+44,GSC,-0.831203544052,1.33813143984,-0.171221212023,-0.826459696747,-0.763419237407,0,-0.27073775959150004,-0.171221212023,-0.09951654756850004,11.0
+45,GSC2,-0.831203544052,-0.8206442490639999,-0.955346518514,-0.826459696747,-0.763419237407,0,-0.8104316818175,-0.955346518514,0.14491483669649996,27.0
+46,HIC1,-0.831203544052,-0.8206442490639999,-0.955346518514,1.8864719526099998,-0.763419237407,0,-0.13219876947825007,-0.955346518514,0.8231477490357499,59.0
+58,KLF14,-0.831203544052,-0.8206442490639999,-0.955346518514,-0.826459696747,-0.763419237407,0,-0.8104316818175,-0.955346518514,0.14491483669649996,27.0
+66,MAFK,1.27759637254,-0.7354105424869999,-0.955346518514,-0.545117906742,0.319945812562,0,0.07925343396825,-0.955346518514,1.03459995248225,61.0
+69,MLX,-0.39860903808,-0.352312943782,-0.7122370061390001,-0.826459696747,-0.691220547486,0,-0.56715055652375,-0.7122370061390001,0.14508644961525008,37.0
+70,MTF1,-0.10904927370100001,-0.29435656592500004,-0.0519983655507,-0.22471788155,-0.763419237407,0,-0.34788573964575,-0.0519983655507,-0.29588737409505,5.0
+74,NFIC,-0.147380548433,0.143199397263,-0.157693908629,-0.826459696747,-0.12347141042000001,0,-0.23852806458425,-0.157693908629,-0.08083415595524998,14.0
+75,NFIX,-0.831203544052,-0.8206442490639999,-0.955346518514,-0.826459696747,-0.763419237407,0,-0.8104316818175,-0.955346518514,0.14491483669649996,27.0
+76,NKX2-3,-0.831203544052,-0.8206442490639999,-0.0294886136988,-0.826459696747,-0.763419237407,0,-0.8104316818175,-0.0294886136988,-0.7809430681187001,1.0
+78,NR1H3,0.344504992736,0.21124022266399997,-0.1645435805,-0.509326935122,-0.763419237407,0,-0.17925023928225,-0.1645435805,-0.014706658782249998,17.0
+81,NR2F6,0.0469024459779,0.19875440244800002,-0.955346518514,0.8481536256190001,-0.308918414009,0,0.19622301500897504,-0.955346518514,1.151569533522975,63.0
+82,NR4A2,-0.831203544052,-0.8206442490639999,-0.955346518514,-0.09403872341649999,0.8288819141179999,0,-0.229251150603625,-0.955346518514,0.726095367910375,55.0
+83,NRF1,-0.215972139588,-0.27755317522100004,0.11360987992,-0.6883505301549999,-0.763419237407,0,-0.48632377059275,0.11360987992,-0.59993365051275,2.0
+90,PAX5,-0.831203544052,-0.8206442490639999,-0.955346518514,-0.826459696747,-0.763419237407,0,-0.8104316818175,-0.955346518514,0.14491483669649996,27.0
+91,PAX6,-0.831203544052,-0.440616538773,-0.955346518514,-0.826459696747,0.33162447432500003,0,-0.44166382631175,-0.955346518514,0.5136826922022499,48.0
+94,PITX3,-0.831203544052,-0.8206442490639999,-0.955346518514,-0.826459696747,-0.763419237407,0,-0.8104316818175,-0.955346518514,0.14491483669649996,27.0
+98,RARA,-0.831203544052,-0.426337617547,-0.5191478523699999,0.58159477942,0.0691922118761,0,-0.15168854257572498,-0.5191478523699999,0.367459309794275,46.0
+103,RFX1,0.38517802445200006,0.237903767304,-0.9521139055560001,-0.826459696747,-0.61830466648,0,-0.20542064286775,-0.9521139055560001,0.7466932626882501,56.0
+107,RXRB,-0.831203544052,0.9059567969169999,-0.6588265959049999,0.065274373862,0.477977122657,0,0.15450118734599996,-0.6588265959049999,0.8133277832509999,58.0
+109,SIX3,-0.831203544052,0.0053171975959499995,-0.955346518514,-0.826459696747,-0.763419237407,0,-0.6039413201525126,-0.955346518514,0.3514051983614874,44.0
+110,SMAD2,-0.511815141672,-0.0727774255295,-0.757269409003,-0.763460701207,-0.763419237407,0,-0.527868126453875,-0.757269409003,0.22940128254912495,40.0
+111,SMAD3,-0.103370493511,-0.512116050849,-0.955346518514,-0.49239101435000004,0.154252442304,0,-0.2384062791015,-0.955346518514,0.7169402394125,54.0
+112,SMAD4,-0.7438853658660001,-0.663839786452,-0.21643693873599998,-0.776913164979,-0.763419237407,0,-0.737014388676,-0.21643693873599998,-0.52057744994,4.0
+114,SOX10,-0.167107548588,-0.07293750367339999,-0.740442508403,-0.826459696747,-0.763419237407,0,-0.45748099660385,-0.740442508403,0.28296151179914997,42.0
+115,SOX11,-0.645055831143,-0.8206442490639999,-0.205256298247,0.053793856269399996,-0.5317592206589999,0,-0.48591636114914993,-0.205256298247,-0.28066006290214995,6.0
+116,SOX4,-0.6557479440649999,-0.8206442490639999,-0.21971502002300003,0.0498881423596,-0.05672091293480001,0,-0.37080624092604997,-0.21971502002300003,-0.15109122090304994,10.0
+117,SOX8,-0.132633896182,-0.364127695068,-0.955346518514,-0.618913585735,-0.52812776344,0,-0.41095073510625,-0.955346518514,0.54439578340775,50.0
+123,SPZ1,-0.831203544052,-0.8206442490639999,-0.955346518514,-0.826459696747,-0.763419237407,0,-0.8104316818175,-0.955346518514,0.14491483669649996,27.0
+124,SREBF1,-0.12529784657,0.267146182489,-0.27101004938,-0.826459696747,-0.762787186431,0,-0.36184963681475,-0.27101004938,-0.09083958743475001,13.0
+125,SREBF2,0.190689330777,0.0345036388095,-0.0992332576143,-0.5862485840439999,-0.763419237407,0,-0.281118712966125,-0.0992332576143,-0.181885455351825,9.0
+128,STAT3,1.8408406073299999,-0.405941988661,-0.955346518514,-0.071748997052,-0.0292730511926,0,0.33346914260609994,-0.955346518514,1.2888156611201,64.0
+130,TBX15,-0.831203544052,-0.8206442490639999,-0.955346518514,-0.826459696747,-0.763419237407,0,-0.8104316818175,-0.955346518514,0.14491483669649996,27.0
+135,TFAP2B,-0.831203544052,-0.8206442490639999,-0.955346518514,-0.826459696747,-0.763419237407,0,-0.8104316818175,-0.955346518514,0.14491483669649996,27.0
+137,TFE3,1.3625738679,-0.34707639591899997,-0.955346518514,0.00150637185734,-0.275591636831,0,0.18535305175183497,-0.955346518514,1.140699570265835,62.0
+138,TFEB,1.40293825727,-0.8206442490639999,-0.955346518514,-0.571674246534,-0.6636645087259999,0,-0.16326118676349996,-0.955346518514,0.7920853317505,57.0
+139,TFEC,-0.831203544052,-0.8206442490639999,-0.955346518514,-0.826459696747,-0.763419237407,0,-0.8104316818175,-0.955346518514,0.14491483669649996,27.0
+140,TLX1,-0.831203544052,-0.8206442490639999,-0.955346518514,-0.826459696747,-0.763419237407,0,-0.8104316818175,-0.955346518514,0.14491483669649996,27.0
+141,TP53,1.40069723154,-0.658096632153,-0.0963264156335,-0.611202144811,-0.763419237407,0,-0.15800519570775,-0.0963264156335,-0.06167878007425001,16.0
+142,USF1,-0.0903272941752,-0.726178881275,0.109200708772,0.977082438275,-0.763419237407,0,-0.15071074364555,0.109200708772,-0.25991145241755,7.0
+143,VDR,-0.381017082257,-0.8206442490639999,-0.955346518514,-0.826459696747,-0.763419237407,0,-0.69788506636875,-0.955346518514,0.25746145214524996,41.0
+144,XBP1,-0.598968468314,-0.440243075965,-0.0267631158108,-0.826459696747,-0.38710224748899996,0,-0.56319337212875,-0.0267631158108,-0.5364302563179499,3.0
+145,YY1,0.06569437705719999,-0.0810338369828,-0.0681535871786,-0.826459696747,-0.342060289337,0,-0.29596486150240003,-0.0681535871786,-0.22781127432380005,8.0
+146,ZBTB7B,0.659281504797,-0.14858615333699998,-0.415279833424,-0.5521833544070001,-0.763419237407,0,-0.20122681008850002,-0.415279833424,0.21405302333549997,39.0
+148,ZEB1,-0.831203544052,-0.8206442490639999,-0.955346518514,-0.826459696747,-0.763419237407,0,-0.8104316818175,-0.955346518514,0.14491483669649996,27.0
+150,ZIC1,-0.831203544052,-0.8206442490639999,-0.955346518514,-0.826459696747,-0.763419237407,0,-0.8104316818175,-0.955346518514,0.14491483669649996,27.0
+152,ZIC4,-0.831203544052,-0.8206442490639999,-0.955346518514,-0.826459696747,-0.763419237407,0,-0.8104316818175,-0.955346518514,0.14491483669649996,27.0

analysis/GRO_seq_TFSEE/cluster2_enriched_tfs.csv

+,Unnamed: 0,ES_D0,ES_D2,ES_D5,ES_D7,ES_D10,cluster,early,late,diff,rank
+15,DMBX1,-0.831203544052,-0.8206442490639999,1.53315994032,-0.826459696747,-0.763419237407,1,-0.8104316818175,1.53315994032,2.3435916221375,24.0
+26,ELF4,0.6451788423170001,-0.000427788120375,0.7362349227670001,-0.826459696747,0.886010205068,1,0.17607539062940625,0.7362349227670001,0.5601595321375938,5.0
+47,HIC2,-0.831203544052,0.7736306889679999,1.07363997237,-0.477988723118,-0.505046929662,1,-0.26015212696600004,1.07363997237,1.3337920993360002,13.0
+49,ID4,-0.588674445025,-0.8206442490639999,1.47425293697,0.04362218980819999,1.72678981973,1,0.09027332886230005,1.47425293697,1.3839796081076998,15.0
+57,KLF12,-0.831203544052,-0.793287265588,1.6094174637600003,-0.330769767438,-0.14852387826400001,1,-0.5259461138355,1.6094174637600003,2.1353635775955,23.0
+62,MAF,-0.27713128163,-0.8206442490639999,0.88750664286,1.14292425782,0.6630169020960001,1,0.17704140730550008,0.88750664286,0.7104652355544999,7.0
+71,MZF1,-0.831203544052,-0.177906355619,0.27090903732,0.70989778546,0.254683787546,1,-0.011132081666249974,0.27090903732,0.28204111898624995,1.0
+73,NFE2L2,-0.831203544052,0.478728873059,0.618376855418,1.59138862747,-0.641509117251,1,0.1493512098065,0.618376855418,0.46902564561150006,4.0
+77,NKX2-8,-0.831203544052,-0.8206442490639999,0.8474457127089999,-0.826459696747,-0.763419237407,1,-0.8104316818175,0.8474457127089999,1.6578773945265,20.0
+87,OTX1,-0.831203544052,0.561246152713,1.2284735789599999,-0.281243574422,-0.763419237407,1,-0.32865505079199997,1.2284735789599999,1.557128629752,17.0
+89,PAX1,-0.831203544052,-0.8206442490639999,0.8450484219869999,0.5526016838660001,-0.763419237407,1,-0.46566633666425006,0.8450484219869999,1.31071475865125,12.0
+92,PAX9,-0.831203544052,-0.8206442490639999,0.670931307875,-0.826459696747,-0.763419237407,1,-0.8104316818175,0.670931307875,1.4813629896925,16.0
+97,PRDM1,-0.831203544052,0.694266905221,0.583070550639,0.5614852440820001,-0.763419237407,1,-0.084717658039,0.583070550639,0.667788208678,6.0
+99,RARB,-0.831203544052,1.10038786441,0.952941964517,1.5564911929499998,0.203001439264,1,0.507169238143,0.952941964517,0.445772726374,3.0
+101,REL,-0.831203544052,-0.141135157238,1.01523434568,0.68092708426,-0.0466431429927,1,-0.08451369000567499,1.01523434568,1.0997480356856748,10.0
+104,RHOXF1,-0.831203544052,-0.8206442490639999,0.925794367404,1.09412498129,-0.142671367057,1,-0.17509854472075,0.925794367404,1.10089291212475,11.0
+106,RXRA,-0.831203544052,0.208194046865,1.11256063726,-0.328341820425,-0.06182302703430001,1,-0.25329358616157505,1.11256063726,1.3658542234215751,14.0
+108,RXRG,-0.831203544052,0.908858186274,0.421505186322,-0.826459696747,0.941597911266,1,0.04819821418524997,0.421505186322,0.37330697213675,2.0
+113,SNAI2,-0.831203544052,-0.8206442490639999,1.35448088488,-0.826459696747,1.4535671603100002,1,-0.25618508238824994,1.35448088488,1.61066596726825,19.0
+120,SP3,-0.216198487993,-0.653178524609,1.40542230343,-0.503033746777,-0.763419237407,1,-0.5339574991965,1.40542230343,1.9393798026265001,21.0
+131,TCF3,-0.538211651816,0.31660837041400003,0.824596358822,-0.826459696747,0.626825184785,1,-0.10530944834099995,0.824596358822,0.929905807163,9.0
+133,TEAD3,-0.251087498855,-0.8206442490639999,0.6371037818399999,-0.528812980185,0.670735802536,1,-0.232452231392,0.6371037818399999,0.8695560132319999,8.0
+134,TFAP2A,-0.831203544052,-0.8206442490639999,1.5940219270299998,-0.826459696747,0.5952994437520001,1,-0.47075201152775,1.5940219270299998,2.06477393855775,22.0
+155,ZNF354C,0.308711507241,0.010222562117799998,1.5072781093399998,0.0945755415552,-0.763419237407,1,-0.08747740662325001,1.5072781093399998,1.5947555159632498,18.0

analysis/GRO_seq_TFSEE/cluster3_enriched_tfs.csv

+,Unnamed: 0,ES_D0,ES_D2,ES_D5,ES_D7,ES_D10,cluster,early,late,diff,rank
+2,ATF4,-0.128229266931,0.771384267987,0.889629220468,-0.570708341734,-0.763419237407,2,0.5109280738413333,-0.6670637895705,1.1779918634118334,12.0
+3,BACH1,1.7635529745599996,1.45203215811,1.3401416389,1.00655861377,-0.763419237407,2,1.518575590523333,0.12156968818149999,1.3970059023418329,18.0
+9,CENPB,1.71020800903,0.21023334164000002,1.4424033624700001,-0.826459696747,0.143069731692,2,1.1209482377133335,-0.3416949825275,1.4626432202408335,20.0
+10,CREB1,1.32311147014,0.7951088526060001,0.66418182297,-0.252826947829,-0.763419237407,2,0.9274673819053333,-0.508123092618,1.4355904745233334,19.0
+13,CTCF,0.8811008062729999,0.62463639338,0.901144241981,-0.826459696747,0.162886087879,2,0.8022938138779999,-0.331786804434,1.1340806183119998,10.0
+16,E2F4,0.686007108025,-0.034963318354300006,0.507351479767,-0.826459696747,-0.530269445639,2,0.3861317564792333,-0.678364571193,1.0644963276722332,8.0
+17,E2F6,1.46351972449,1.0223216572299998,0.928910532797,0.266251882512,-0.763419237407,2,1.1382506381723332,-0.2485836774475,1.3868343156198333,17.0
+18,E2F8,1.4927943285799998,-0.19701988974399998,0.723721762435,-0.826459696747,0.907900185462,2,0.6731654004236666,0.04072024435749999,0.6324451560661666,3.0
+28,ELK4,1.2268924864200002,0.600154136127,0.899149911524,-0.826459696747,-0.629155864639,2,0.9087321780236667,-0.727807780693,1.6365399587166667,27.0
+35,FOXD3,3.56676798797,2.74503498134,-0.955346518514,-0.826459696747,-0.763419237407,2,1.7854854835986664,-0.794939467077,2.5804249506756665,34.0
+36,FOXJ3,0.160197528421,0.892009602361,2.5121397021200003,3.1280983816,-0.763419237407,2,1.1881156109673334,1.1823395720965,0.005776038870833444,1.0
+37,FOXK1,-0.831203544052,5.62366290652,4.4251306484,0.666792163315,1.24890927054,2,3.0725300036226666,0.9578507169275,2.1146792866951665,30.0
+39,GABPA,0.565646243636,0.945576710579,0.358822292576,-0.6179353019389999,-0.763419237407,2,0.623348415597,-0.6906772696729999,1.3140256852699999,15.0
+42,GLI2,1.60853347262,0.8177576729000001,0.0857049073638,-0.826459696747,-0.140411784108,2,0.8373320176279333,-0.48343574042750004,1.3207677580554333,16.0
+48,HINFP,1.63013720849,1.7934546042,1.66414186815,1.05351941926,-0.763419237407,2,1.6959112269466665,0.14505009092649995,1.5508611360201665,25.0
+52,IRF2,1.4879537692200002,0.40914511145000004,0.151992124811,0.432237819351,-0.763419237407,2,0.6830303351603334,-0.16559070902800002,0.8486210441883334,4.0
+56,KLF1,-0.831203544052,1.9990830141099998,2.17555171415,0.0500004906673,-0.763419237407,2,1.1144770614026667,-0.35670937336985,1.4711864347725165,21.0
+59,KLF16,2.00504098097,1.9376202164900003,0.7981671712289999,-0.669919225884,-0.763419237407,2,1.5802761228963336,-0.7166692316455,2.2969453545418337,31.0
+65,MAFG,1.65463539038,1.86803053164,-0.23973228783300002,-0.023692892895999997,-0.763419237407,2,1.0943112113956666,-0.3935560651515,1.4878672765471666,22.0
+79,NR2C2,2.0938567538,1.59523719675,1.60254774643,-0.48764627157799995,-0.763419237407,2,1.76388056566,-0.6255327544925,2.3894133201525003,33.0
+84,NRL,0.629557573151,0.905587783994,0.018359627253,-0.826459696747,-0.127407865953,2,0.5178349947993334,-0.47693378135000003,0.9947687761493333,6.0
+88,OTX2,0.35011117908,1.3118364241,0.379012005155,-0.328494433893,-0.763419237407,2,0.680319869445,-0.54595683565,1.226276705095,14.0
+95,PLAG1,1.2235431601,1.03703066502,1.12651433504,1.16765208615,-0.763419237407,2,1.1290293867199999,0.20211642437149996,0.9269129623485,5.0
+100,RARG,1.41413943991,1.18754482231,0.566077937083,-0.280872503026,-0.763419237407,2,1.055920733101,-0.5221458702165,1.5780666033175001,26.0
+102,REST,0.207565878549,0.950519091181,1.10986496985,0.197171705605,-0.763419237407,2,0.7559833131933335,-0.283123765901,1.0391070790943335,7.0
+118,SP1,-0.010595069584200001,2.46572945825,1.44701673887,-0.826459696747,-0.5707682341179999,2,1.3007170425119332,-0.6986139654325,1.9993310079444333,29.0
+119,SP2,0.980451524639,0.7752367373219999,1.92645823218,-0.826459696747,1.03594394061,2,1.2273821647136665,0.10474212193149995,1.1226400427821666,9.0
+121,SP4,1.5746857305200002,-0.47674791127800004,0.316833997627,-0.826459696747,-0.676118844411,2,0.4715906056230001,-0.751289270579,1.2228798762020001,13.0
+122,SP8,1.8875637899900002,1.87327578992,1.01002375543,-0.826459696747,-0.763419237407,2,1.590287778446667,-0.794939467077,2.3852272455236667,32.0
+132,TCF4,1.0556968812,-0.136149513454,0.528222521152,0.968576023849,-0.763419237407,2,0.482589962966,0.10257839322099999,0.380011569745,2.0
+136,TFAP4,0.434696718275,0.170812091078,0.557345373408,-0.73047586287,-0.763419237407,2,0.3876180609203333,-0.7469475501385,1.1345656110588334,11.0
+151,ZIC3,1.83897875692,2.1540618863,0.8971278819930001,0.14706490929899999,-0.763419237407,2,1.630056175071,-0.30817716405400003,1.9382333391250002,28.0
+153,ZNF143,0.592441979321,1.4562589119100002,0.24670261390099998,-0.7733827243860001,-0.763419237407,2,0.7651345017106667,-0.7684009808965,1.5335354826071668,24.0
+154,ZNF263,0.9930237214650001,0.457644077801,1.17743761776,-0.826459696747,-0.407327039775,2,0.8760351390086667,-0.616893368261,1.4929285072696667,23.0

analysis/GRO_seq_TFSEE/cluster4_enriched_tfs.csv

+,Unnamed: 0,ES_D0,ES_D2,ES_D5,ES_D7,ES_D10,cluster,early,late,diff,rank
+1,ARNTL,1.43844896065,0.526692185861,-0.955346518514,0.23443327818100002,0.609255929363,3,0.33659820933233325,0.421844603772,0.08524639443966675,2.0
+4,CEBPA,0.86625282574,-0.8206442490639999,0.571220397017,1.00317776452,0.55720839998,3,0.2056096578976667,0.7801930822500001,0.5745834243523333,5.0
+11,CREB3,0.347928730664,0.5324674009839999,-0.955346518514,1.60255994632,1.18483389894,3,-0.024983462288666696,1.39369692263,1.4186803849186667,16.0
+12,CREB3L1,0.670981944029,-0.8206442490639999,0.640984388356,1.4754070694699999,0.107089472761,3,0.1637740277736667,0.7912482711155,0.6274742433418333,7.0
+19,EGR1,1.4377017070200002,0.39670512930299995,-0.955346518514,2.46049955426,2.19696217147,3,0.2930201059363334,2.328730862865,2.0357107569286668,28.0
+23,EHF,-0.831203544052,-0.8206442490639999,-0.955346518514,0.8062843263989999,0.998598392005,3,-0.8690647705433333,0.902441359202,1.7715061297453332,23.0
+24,ELF1,-0.831203544052,-0.0282116640913,-0.744081576418,0.853893460563,0.986363127414,3,-0.5344989281871001,0.9201282939885,1.4546272221756,17.0
+27,ELF5,-0.831203544052,-0.8206442490639999,-0.955346518514,0.969893831628,1.54703018579,3,-0.8690647705433333,1.258462008709,2.1275267792523334,30.0
+32,FOS,1.1182705897,-0.202710621966,-0.955346518514,0.143275958374,1.3334499527399999,3,-0.01326218359333331,0.7383629555569999,0.7516251391503332,9.0
+38,FOXP1,0.107430363159,-0.8206442490639999,2.66443753433,3.7309585815300004,3.7953445307699996,3,0.6504078828083334,3.76315155615,3.1127436733416665,33.0
+43,GLIS2,0.719811476962,-0.8206442490639999,0.609984073152,1.7686556340900002,0.11186979890599999,3,0.16971710035,0.9402627164980001,0.7705456161480001,10.0
+50,INSM1,-0.831203544052,-0.8206442490639999,0.0104560813663,0.872312396347,1.8280915122299999,3,-0.5471305705832333,1.3502019542885,1.8973325248717332,24.0
+51,IRF1,3.1134183136,2.83451415432,-0.955346518514,2.4237492535599996,1.97776928403,3,1.6641953164686665,2.2007592687949997,0.5365639523263332,3.0
+53,IRF8,-0.831203544052,-0.8206442490639999,-0.955346518514,0.47572463306699997,0.973020876937,3,-0.8690647705433333,0.724372755002,1.5934375255453332,20.0
+54,JUN,1.49267952178,0.167442366712,-0.955346518514,0.828173309552,0.788756791907,3,0.234925123326,0.8084650507294999,0.5735399274034999,4.0
+55,JUNB,1.3714003593900002,0.342461940729,-0.948311441067,-0.826459696747,1.3366074939,3,0.255183619684,0.25507389857650004,-0.00010972110749996045,1.0
+60,KLF4,2.4767204621000003,-0.8206442490639999,-0.955346518514,1.40534725569,0.298405676749,3,0.23357656484066683,0.8518764662195,0.6182999013788332,6.0
+61,KLF5,-0.831203544052,1.9183958451400003,0.10560438074100001,1.7229830912400002,3.09936322446,3,0.39759889394300013,2.41117315785,2.013574263907,27.0
+63,MAFB,0.162505006883,-0.8206442490639999,-0.024682762782,0.19838272480900002,1.4454383976499998,3,-0.22760733498766664,0.8219105612294999,1.0495178962171665,13.0
+64,MAFF,0.933922999206,0.8935454733020001,-0.955346518514,1.6749360596,2.03732208042,3,0.290707317998,1.8561290700100002,1.5654217520120002,19.0
+67,MECOM,-0.831203544052,-0.8206442490639999,0.842137622249,3.31476987871,2.55268035989,3,-0.269903390289,2.9337251193,3.203628509589,34.0
+68,MITF,-0.831203544052,-0.8206442490639999,-0.955346518514,1.25712028692,1.08765626935,3,-0.8690647705433333,1.1723882781350001,2.0414530486783335,29.0
+72,NFE2,-0.45788525044100004,-0.8206442490639999,-0.0411450252305,0.29631698905000003,1.3760005188,3,-0.4398915082451666,0.8361587539249999,1.2760502621701666,14.0
+80,NR2F1,-0.831203544052,-0.8206442490639999,-0.955346518514,1.19334347744,1.35148238509,3,-0.8690647705433333,1.2724129312649999,2.1414777018083333,31.0
+85,ONECUT2,-0.831203544052,-0.22679474172800002,-0.955346518514,1.08772197115,1.5146269376600001,3,-0.6711149347646668,1.301174454405,1.9722893891696667,26.0
+86,ONECUT3,-0.831203544052,-0.8206442490639999,-0.955346518514,-0.826459696747,3.6444844220499997,3,-0.8690647705433333,1.4090123626514999,2.278077133194833,32.0
+93,PITX1,-0.831203544052,-0.8206442490639999,1.2817375287100001,2.21897666824,1.41580084299,3,-0.1233700881353333,1.817388755615,1.9407588437503331,25.0
+96,PPARG,-0.831203544052,-0.8206442490639999,0.9739286783059999,1.12376928597,1.67839254243,3,-0.22597303827000004,1.4010809142,1.62705395247,21.0
+105,RUNX1,-0.831203544052,-0.8206442490639999,-0.955346518514,0.48772869053499995,0.8666475520069999,3,-0.8690647705433333,0.6771881212709999,1.5462528918143332,18.0
+126,STAT1,-0.6113575256530001,0.0848502745951,-0.5670212309730001,-0.826459696747,2.13131094678,3,-0.36450949401030003,0.6524256250165001,1.0169351190268001,12.0
+127,STAT2,-0.831203544052,0.520551637768,0.316908158112,1.7484554316999998,0.820400226534,3,0.002085417275999979,1.284427829117,1.2823424118409998,15.0
+129,STAT4,-0.831203544052,0.884903238187,-0.955346518514,-0.826459696747,1.58264408926,3,-0.30054894145966665,0.3780921962565,0.6786411377161666,8.0
+147,ZBTB7C,-0.831203544052,1.1785215961700002,-0.955346518514,1.90587724343,0.963089338766,3,-0.20267615546533327,1.434483291098,1.6371594465633335,22.0
+149,ZFX,0.115269594414,-0.298669024804,-0.955346518514,0.09379201306160001,1.08294534249,3,-0.379581982968,0.5883686777757999,0.9679506607438,11.0

analysis/GRO_seq_TFSEE/cluster_1_tfs.csv

+symbol,ES_D0,ES_D2,ES_D5,ES_D7,ES_D10
+AR,2.645,0.195,1.255,0.755,0.73
+CEBPB,8.0,5.345,3.44,2.54,2.92
+CEBPD,0.84,0.895,0.365,0.25,0.435
+CEBPE,0.005,0.015,0.01,0.0,0.015
+CEBPG,8.805,9.6,10.255,10.94,10.555
+DDIT3,3.545,7.775,6.02,10.41,8.37
+EGR2,0.39,0.005,0.005,0.49,0.305
+EGR3,0.02,0.09,0.025,1.28,0.49
+EGR4,0.005,0.005,0.01,0.425,0.205
+ELF3,2.21,3.685,3.88,52.51,13.54
+ESR1,0.045,0.065,0.03,0.205,0.26
+ESR2,0.28,0.155,0.28,0.415,0.68
+FIGLA,0.015,0.0,0.0,0.0,0.0
+FOSL2,1.235,0.795,1.185,50.66,7.785
+FOXC2,0.07,0.005,0.01,0.175,0.32
+GCM2,0.08,0.045,0.035,0.005,0.02
+GFI1B,0.0,0.015,0.0,0.0,0.01
+GSC,0.25,204.8,0.555,0.09,0.055
+GSC2,0.1,0.0,0.0,0.0,0.015
+HIC1,0.145,0.165,0.065,0.605,0.385
+KLF14,0.03,0.025,0.0,0.0,0.03
+MAFK,4.18,2.8,3.395,5.395,7.09
+MLX,28.085,30.715,18.125,17.77,22.08
+MTF1,2.85,3.065,4.065,5.195,4.16
+NFIC,2.17,4.23,4.19,2.34,4.375
+NFIX,0.055,0.025,0.02,0.335,0.205
+NKX2-3,0.0,0.0,4.155,0.005,0.0
+NR1H3,17.065,15.795,9.21,9.02,7.935
+NR2F6,61.655,57.925,41.47,93.865,67.675
+NR4A2,0.06,0.185,0.215,0.595,1.415
+NRF1,12.775,12.645,15.66,15.51,16.51
+PAX5,0.055,0.0,0.03,0.005,0.025
+PAX6,0.145,0.58,0.07,0.135,25.865
+PITX3,0.07,0.115,0.02,0.0,0.01
+RARA,6.195,10.955,11.025,33.47,26.135
+RFX1,10.79,10.71,6.615,9.515,11.335
+RXRB,8.365,11.415,10.39,15.91,18.145
+SIX3,0.005,6.42,0.105,0.015,0.025
+SMAD2,33.815,63.24,29.905,33.295,33.98
+SMAD3,18.595,12.95,10.205,20.925,35.53
+SMAD4,54.035,47.595,59.69,60.76,66.16
+SOX10,2.095,13.225,0.425,0.18,0.285
+SOX11,6.49,3.32,31.61,65.87,13.725
+SOX4,89.935,50.825,149.125,233.1,229.0
+SOX8,4.705,1.955,0.19,0.72,1.02
+SPZ1,0.025,0.0,0.0,0.0,0.0
+SREBF1,19.795,25.405,19.81,19.805,22.11
+SREBF2,96.135,75.58,60.99,36.32,32.135
+STAT3,27.22,8.29,7.995,15.825,16.81
+TBX15,0.02,0.015,0.01,0.035,0.005
+TFAP2B,0.0,0.0,0.055,0.015,0.01
+TFE3,29.7,10.12,8.635,18.995,17.13
+TFEB,0.88,0.18,0.235,0.5,0.5
+TFEC,0.0,0.0,0.0,0.005,0.005
+TLX1,0.0,0.0,0.015,0.0,0.005
+TP53,103.305,35.18,51.03,48.995,49.785
+USF1,26.51,20.425,28.505,43.945,32.515
+VDR,0.425,0.055,0.095,0.085,0.175
+XBP1,62.435,68.655,96.21,51.89,85.765
+YY1,67.84,55.3,61.2,49.025,62.51
+ZBTB7B,12.2,9.37,10.2,12.825,13.09
+ZEB1,0.035,0.31,0.0,0.155,0.36
+ZIC1,0.115,0.12,0.16,0.07,0.06
+ZIC4,0.02,0.0,0.0,0.025,0.045