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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4115_mesothelioma_chorionic_Smooth_Sertoli_Prostate_Mesenchymal_tubular
|full_id=C4115_mesothelioma_chorionic_Smooth_Sertoli_Prostate_Mesenchymal_tubular
|id=C4115
|id=C4115

Revision as of 17:09, 12 September 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><br>

Uber Anatomy
Ontology termp-valuen
vasculature1.08e-2179
vascular system1.08e-2179
artery5.42e-1942
arterial blood vessel5.42e-1942
arterial system5.42e-1942
blood vessel7.93e-1960
epithelial tube open at both ends7.93e-1960
blood vasculature7.93e-1960
vascular cord7.93e-1960
splanchnic layer of lateral plate mesoderm1.42e-1884
vessel1.48e-1869
epithelial tube1.37e-16118
unilaminar epithelium5.54e-16138
systemic artery1.27e-1533
systemic arterial system1.27e-1533
cardiovascular system1.78e-15110
circulatory system4.33e-15113
skeletal muscle tissue4.81e-1461
striated muscle tissue4.81e-1461
myotome4.81e-1461
muscle tissue1.33e-1363
musculature1.33e-1363
musculature of body1.33e-1363
somite3.84e-1383
paraxial mesoderm3.84e-1383
presomitic mesoderm3.84e-1383
presumptive segmental plate3.84e-1383
trunk paraxial mesoderm3.84e-1383
presumptive paraxial mesoderm3.84e-1383
trunk mesenchyme1.56e-12143
dermomyotome6.30e-1270
multilaminar epithelium3.29e-1182
trunk1.52e-10216
aorta4.31e-1021
aortic system4.31e-1021
mesenchyme6.03e-10238
entire embryonic mesenchyme6.03e-10238
anatomical cluster7.48e-10286
multi-tissue structure1.30e-08347
mesoderm1.76e-07448
mesoderm-derived structure1.76e-07448
presumptive mesoderm1.76e-07448
organism subdivision4.30e-07365
multi-cellular organism9.47e-07659
anatomical conduit9.81e-07241


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.

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