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Coexpression cluster:C2967: Difference between revisions

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|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0114864691848068!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0166716843266346!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00242189627049967!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.0057906056624429!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.00106995413460918!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00432526036681602!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00389671093746339!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00122414128686165!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000754787472264016!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00442862492801277!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185587471442757!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00717886319120292!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0292960126655378!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00307700001623022!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00164783505949838!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245256588129722!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00641250870807095!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00611265358800226!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00247197994315821!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00612502478424388!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189359216410087!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00420242938102566
|tf_chipseq_enrich=CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0114864691848068!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0166716843266346!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00242189627049967!FOXA1#3169;3:11.0814197493855:0.00073475527569867:0.0057906056624429!FOXA2#3170;3:24.6304637526652:6.68983856509345e-05:0.00106995413460918!GTF2F1#2962;3:12.7396608767577:0.000483552504743859:0.00432526036681602!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00389671093746339!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00122414128686165!HNF4G#3174;3:28.7534225264468:4.20470658818262e-05:0.000754787472264016!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00442862492801277!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0185587471442757!MXI1#4601;3:9.9615716287593:0.00101147054125902:0.00717886319120292!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0292960126655378!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00307700001623022!RXRA#6256;3:20.0746171391333:0.000123573034843222:0.00164783505949838!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0245256588129722!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00641250870807095!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00611265358800226!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00247197994315821!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00612502478424388!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189359216410087!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00420242938102566
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}}
}}

Revision as of 15:50, 26 November 2012


Full id: C2967_lung_Hepatocyte_hepatoma_hepatocellular_liver_mesothelioma_Intestinal



Phase1 CAGE Peaks

Hg19::chr10:101542462..101542535,+p1@ABCC2
Hg19::chr10:101542550..101542573,+p5@ABCC2
Hg19::chr10:101542585..101542592,+p6@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
metabolising cell9.20e-1912
endopolyploid cell9.20e-1912
parenchymal cell9.20e-1912
polyploid cell9.20e-1912
hepatocyte9.20e-1912
epithelial cell1.07e-12253
melanocyte5.93e-0910
melanoblast5.93e-0910
endodermal cell6.01e-0958
Uber Anatomy
Ontology termp-valuen
larynx7.88e-249
subdivision of digestive tract1.94e-23118
epithelium of foregut-midgut junction3.67e-2025
anatomical boundary3.67e-2025
hepatobiliary system3.67e-2025
foregut-midgut junction3.67e-2025
septum transversum3.67e-2025
hepatic diverticulum4.72e-2022
liver primordium4.72e-2022
liver5.15e-2019
digestive gland5.15e-2019
liver bud5.15e-2019
digestive tract diverticulum4.92e-1923
digestive system1.54e-18145
digestive tract1.54e-18145
primitive gut1.54e-18145
foregut2.78e-1887
epithelial sac3.04e-1725
sac1.88e-1626
endoderm-derived structure7.03e-16160
endoderm7.03e-16160
presumptive endoderm7.03e-16160
abdomen element9.31e-1354
abdominal segment element9.31e-1354
abdominal segment of trunk2.38e-1260
abdomen2.38e-1260
gut epithelium1.01e-1154
exocrine gland3.94e-1131
exocrine system3.94e-1131
upper respiratory tract2.45e-1019
trunk region element4.65e-10101
respiratory primordium1.53e-0938
endoderm of foregut1.53e-0938
endocrine gland1.54e-0935
endocrine system1.76e-0945
endo-epithelium2.43e-0982
intestine3.05e-0917
gastrointestinal system4.96e-0925
organ system subdivision1.63e-08223
subdivision of trunk2.26e-08112
immaterial anatomical entity9.11e-08117
segment of respiratory tract3.65e-0747
primordium8.31e-07160
Disease
Ontology termp-valuen
carcinoma1.31e-21106
cell type cancer3.04e-17143
cancer4.03e-10235
disease of cellular proliferation1.05e-09239


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#105137.971147625824820.001974187055288560.0114864691848068
EP300#203336.77394172622320.003216880500103790.0166716843266346
FOSL2#2355316.93020060456170.0002060162053171620.00242189627049967
FOXA1#3169311.08141974938550.000734755275698670.0057906056624429
FOXA2#3170324.63046375266526.68983856509345e-050.00106995413460918
GTF2F1#2962312.73966087675770.0004835525047438590.00432526036681602
HDAC2#3066313.41562023662630.0004140761399857210.00389671093746339
HNF4A#3172323.13229036295378.07584663437677e-050.00122414128686165
HNF4G#3174328.75342252644684.20470658818262e-050.000754787472264016
JUN#3725312.51282919233630.0005103313992726250.00442862492801277
MAX#414936.452555509007120.003721913834265510.0185587471442757
MXI1#460139.96157162875930.001011470541259020.00717886319120292
MYC#460935.22228187160940.007020843755740150.0292960126655378
NR3C1#2908314.9730233311730.0002978331194675480.00307700001623022
RXRA#6256320.07461713913330.0001235730348432220.00164783505949838
SP1#666735.69838137814090.005403962701712170.0245256588129722
STAT3#6774310.51946499715420.0008589184530415310.00641250870807095
TCF7L2#6934310.77017656313730.0008003181298398380.00611265358800226
TFAP2A#7020316.5186343730450.0002218033880766340.00247197994315821
TFAP2C#7022310.80922860986020.0007916746575753130.00612502478424388
USF1#739136.361499277207960.00388404057290560.0189359216410087
USF2#7392312.99219738506960.0004558979393427810.00420242938102566



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.