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Coexpression cluster:C2031: Difference between revisions

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|tf_chipseq_enrich=CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00267319126948235!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00433310961373218!FOSL2#2355;4:16.9302006045617:1.2165416097647e-05:0.000302943226471663!FOXA1#3169;4:11.0814197493855:6.62943068949433e-05:0.00106847393793225!FOXA2#3170;4:24.6304637526652:2.71504128667089e-06:9.41109183334287e-05!GTF2F1#2962;4:12.7396608767577:3.79492332235515e-05:0.000716057808244715!HDAC2#3066;4:13.4156202366263:3.0859005065161e-05:0.000625438313603794!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0185431171232269!HNF4A#3172;4:23.1322903629537:3.48990320893214e-06:0.000115342405454957!HNF4G#3174;4:28.7534225264468:1.46167379934821e-06:5.65391666407881e-05!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.000741290237132239!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00484215236768504!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142053936471422!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00885347010549182!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.000441624037122714!RXRA#6256;4:20.0746171391333:6.1537798808435e-06:0.000181911864414213!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00682861404438679!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00122802358839242!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321010380233242!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0243356094411906!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115143175359796!TFAP2A#7020;4:16.518634373045:1.34240829060362e-05:0.000325667315824277!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114285112323773!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00506877562218673!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.000679915583718878
|tf_chipseq_enrich=CEBPB#1051;4:7.97114762582482:0.000247638578809083:0.00267319126948235!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00433310961373218!FOSL2#2355;4:16.9302006045617:1.2165416097647e-05:0.000302943226471663!FOXA1#3169;4:11.0814197493855:6.62943068949433e-05:0.00106847393793225!FOXA2#3170;4:24.6304637526652:2.71504128667089e-06:9.41109183334287e-05!GTF2F1#2962;4:12.7396608767577:3.79492332235515e-05:0.000716057808244715!HDAC2#3066;4:13.4156202366263:3.0859005065161e-05:0.000625438313603794!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0185431171232269!HNF4A#3172;4:23.1322903629537:3.48990320893214e-06:0.000115342405454957!HNF4G#3174;4:28.7534225264468:1.46167379934821e-06:5.65391666407881e-05!JUN#3725;4:12.5128291923363:4.07770316866756e-05:0.000741290237132239!MAX#4149;4:6.45255550900712:0.000576761319564549:0.00484215236768504!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142053936471422!MYC#4609;4:5.2222818716094:0.00134430939527274:0.00885347010549182!NR3C1#2908;4:14.973023331173:1.98868032687801e-05:0.000441624037122714!RXRA#6256;4:20.0746171391333:6.1537798808435e-06:0.000181911864414213!SP1#6667;4:5.6983813781409:0.000948260606533398:0.00682861404438679!STAT3#6774;4:10.5194649971542:8.16377768286615e-05:0.00122802358839242!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0321010380233242!TBP#6908;4:3.70677068709639:0.00529637781478435:0.0243356094411906!TCF7L2#6934;4:10.7701765631373:7.42969445082454e-05:0.00115143175359796!TFAP2A#7020;4:16.518634373045:1.34240829060362e-05:0.000325667315824277!TFAP2C#7022;4:10.8092286098602:7.32289634782688e-05:0.00114285112323773!USF1#7391;4:6.36149927720796:0.000610501139914083:0.00506877562218673!USF2#7392;4:12.9921973850696:3.50833029870167e-05:0.000679915583718878
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}}
}}

Revision as of 15:15, 26 November 2012


Full id: C2031_bile_lung_large_epitheloid_mesothelioma_hepatoma_maxillary



Phase1 CAGE Peaks

Hg19::chr10:101542384..101542406,+p2@ABCC2
Hg19::chr10:101542411..101542414,+p7@ABCC2
Hg19::chr10:101542415..101542428,+p4@ABCC2
Hg19::chr10:101542439..101542457,+p3@ABCC2


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell8.75e-13253
metabolising cell5.64e-1212
endopolyploid cell5.64e-1212
parenchymal cell5.64e-1212
polyploid cell5.64e-1212
hepatocyte5.64e-1212
melanocyte1.50e-1110
melanoblast1.50e-1110
epithelial cell of pancreas4.48e-084
endodermal cell7.06e-0858
pigment cell9.03e-0814
light melanocyte8.67e-073
Uber Anatomy
Ontology termp-valuen
larynx4.80e-189
subdivision of digestive tract1.04e-13118
foregut5.17e-1287
epithelium of foregut-midgut junction5.45e-1225
anatomical boundary5.45e-1225
hepatobiliary system5.45e-1225
foregut-midgut junction5.45e-1225
septum transversum5.45e-1225
digestive system2.48e-11145
digestive tract2.48e-11145
primitive gut2.48e-11145
hepatic diverticulum1.54e-1022
liver primordium1.54e-1022
liver2.05e-1019
digestive gland2.05e-1019
liver bud2.05e-1019
digestive tract diverticulum6.03e-1023
endoderm-derived structure6.52e-10160
endoderm6.52e-10160
presumptive endoderm6.52e-10160
epithelial sac6.62e-0925
upper respiratory tract7.11e-0919
sac1.90e-0826
exocrine gland1.72e-0731
exocrine system1.72e-0731
respiratory primordium2.03e-0738
endoderm of foregut2.03e-0738
gut epithelium5.48e-0754
Disease
Ontology termp-valuen
carcinoma3.79e-22106
cell type cancer5.64e-20143
cancer1.67e-11235
disease of cellular proliferation5.87e-11239
pancreatic cancer4.48e-084


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CEBPB#105147.971147625824820.0002476385788090830.00267319126948235
EP300#203346.77394172622320.0004748459821442640.00433310961373218
FOSL2#2355416.93020060456171.2165416097647e-050.000302943226471663
FOXA1#3169411.08141974938556.62943068949433e-050.00106847393793225
FOXA2#3170424.63046375266522.71504128667089e-069.41109183334287e-05
GTF2F1#2962412.73966087675773.79492332235515e-050.000716057808244715
HDAC2#3066413.41562023662633.0859005065161e-050.000625438313603794
HEY1#2346244.040111043105710.00375304636917980.0185431171232269
HNF4A#3172423.13229036295373.48990320893214e-060.000115342405454957
HNF4G#3174428.75342252644681.46167379934821e-065.65391666407881e-05
JUN#3725412.51282919233634.07770316866756e-050.000741290237132239
MAX#414946.452555509007120.0005767613195645490.00484215236768504
MXI1#460149.96157162875930.0001015224754950450.00142053936471422
MYC#460945.22228187160940.001344309395272740.00885347010549182
NR3C1#2908414.9730233311731.98868032687801e-050.000441624037122714
RXRA#6256420.07461713913336.1537798808435e-060.000181911864414213
SP1#666745.69838137814090.0009482606065333980.00682861404438679
STAT3#6774410.51946499715428.16377768286615e-050.00122802358839242
TAF1#687243.343046285745290.008005664898701650.0321010380233242
TBP#690843.706770687096390.005296377814784350.0243356094411906
TCF7L2#6934410.77017656313737.42969445082454e-050.00115143175359796
TFAP2A#7020416.5186343730451.34240829060362e-050.000325667315824277
TFAP2C#7022410.80922860986027.32289634782688e-050.00114285112323773
USF1#739146.361499277207960.0006105011399140830.00506877562218673
USF2#7392412.99219738506963.50833029870167e-050.000679915583718878



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

This analysis result is provided for C0 - C305 clusters.

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