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Coexpression cluster:C4115: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326048575263942!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167732292835916!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00899093341980634!FOSL1#8061;3:39.713579716373:1.59554825631833e-05:0.000371543956168629!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00243422632278754!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00388424340637691!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00437421770798452!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00122985323220717!JUN#3725;3:12.5128291923363:0.000510331399272625:0.004448956678517!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157045223826977!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186908188169859!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00309290973094077!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00203406441507488!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00155039584114005!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00643551074805972!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00614817397295645!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00248657407120391!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00616843550899046
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0326048575263942!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0167732292835916!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00899093341980634!FOSL1#8061;3:39.713579716373:1.59554825631833e-05:0.000371543956168629!FOSL2#2355;3:16.9302006045617:0.000206016205317162:0.00243422632278754!GATA1#2623;3:13.5603081438004:0.000400961596378263:0.00388424340637691!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00437421770798452!HNF4A#3172;3:23.1322903629537:8.07584663437677e-05:0.00122985323220717!JUN#3725;3:12.5128291923363:0.000510331399272625:0.004448956678517!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157045223826977!MAX#4149;3:6.45255550900712:0.00372191383426551:0.0186908188169859!NR3C1#2908;3:14.973023331173:0.000297833119467548:0.00309290973094077!SMARCB1#6598;3:18.2527157811574:0.00016439776067989:0.00203406441507488!STAT1#6772;3:20.7065874971992:0.000112599244104667:0.00155039584114005!STAT3#6774;3:10.5194649971542:0.000858918453041531:0.00643551074805972!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00614817397295645!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00248657407120391!TFAP2C#7022;3:10.8092286098602:0.000791674657575313:0.00616843550899046
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}}
}}

Revision as of 16:33, 26 November 2012


Full id: C4115_mesothelioma_chorionic_Smooth_Sertoli_Prostate_Mesenchymal_tubular



Phase1 CAGE Peaks

Hg19::chr2:106013294..106013307,-p8@FHL2
Hg19::chr2:106013351..106013364,-p9@FHL2
Hg19::chr2:106013400..106013438,-p5@FHL2


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>


Uber Anatomy
Ontology termp-valuen
artery1.18e-2242
arterial blood vessel1.18e-2242
arterial system1.18e-2242
epithelial tube open at both ends6.54e-1959
blood vessel6.54e-1959
blood vasculature6.54e-1959
vascular cord6.54e-1959
splanchnic layer of lateral plate mesoderm9.25e-1883
systemic artery1.69e-1733
systemic arterial system1.69e-1733
vessel2.19e-1668
vasculature2.67e-1678
vascular system2.67e-1678
skeletal muscle tissue7.79e-1562
striated muscle tissue7.79e-1562
myotome7.79e-1562
muscle tissue1.57e-1464
musculature1.57e-1464
musculature of body1.57e-1464
unilaminar epithelium2.03e-12148
somite2.24e-1271
presomitic mesoderm2.24e-1271
presumptive segmental plate2.24e-1271
dermomyotome2.24e-1271
trunk paraxial mesoderm2.24e-1271
epithelial tube2.74e-12117
cardiovascular system3.04e-12109
dense mesenchyme tissue3.21e-1273
paraxial mesoderm5.60e-1272
presumptive paraxial mesoderm5.60e-1272
circulatory system5.82e-12112
multilaminar epithelium1.81e-1183
epithelial vesicle6.22e-1178
aorta1.60e-1021
aortic system1.60e-1021
blood vessel smooth muscle5.56e-0810
arterial system smooth muscle5.56e-0810
artery smooth muscle tissue5.56e-0810
aorta smooth muscle tissue5.56e-0810
trunk mesenchyme6.13e-08122
mesoderm3.41e-07315
mesoderm-derived structure3.41e-07315
presumptive mesoderm3.41e-07315
trunk6.17e-07199
smooth muscle tissue7.09e-0715
Disease
Ontology termp-valuen
ovarian cancer3.70e-0714


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
E2F1#186934.907389214879320.008460985347239390.0326048575263942
EP300#203336.77394172622320.003216880500103790.0167732292835916
FOS#235338.99795530889440.001372499272417130.00899093341980634
FOSL1#8061339.7135797163731.59554825631833e-050.000371543956168629
FOSL2#2355316.93020060456170.0002060162053171620.00243422632278754
GATA1#2623313.56030814380040.0004009615963782630.00388424340637691
GATA2#2624312.7449317335540.0004829527704283790.00437421770798452
HNF4A#3172323.13229036295378.07584663437677e-050.00122985323220717
JUN#3725312.51282919233630.0005103313992726250.004448956678517
JUND#372736.994663941871030.002921845042734990.0157045223826977
MAX#414936.452555509007120.003721913834265510.0186908188169859
NR3C1#2908314.9730233311730.0002978331194675480.00309290973094077
SMARCB1#6598318.25271578115740.000164397760679890.00203406441507488
STAT1#6772320.70658749719920.0001125992441046670.00155039584114005
STAT3#6774310.51946499715420.0008589184530415310.00643551074805972
TCF7L2#6934310.77017656313730.0008003181298398380.00614817397295645
TFAP2A#7020316.5186343730450.0002218033880766340.00248657407120391
TFAP2C#7022310.80922860986020.0007916746575753130.00616843550899046



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.