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Coexpression cluster:C834: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007524!1.33e-14!73;UBERON:0002329!2.50e-14!71;UBERON:0003059!2.50e-14!71;UBERON:0007282!2.50e-14!71;UBERON:0004290!2.50e-14!71;UBERON:0009618!2.50e-14!71;UBERON:0003077!6.59e-14!72;UBERON:0007285!6.59e-14!72;UBERON:0001134!2.61e-13!62;UBERON:0002036!2.61e-13!62;UBERON:0003082!2.61e-13!62;UBERON:0002385!4.22e-13!64;UBERON:0001015!4.22e-13!64;UBERON:0000383!4.22e-13!64;UBERON:0000486!5.47e-13!83;UBERON:0007503!2.19e-12!78;UBERON:0004923!2.57e-11!66;UBERON:0004872!7.22e-11!83;UBERON:0002199!7.41e-11!46;UBERON:0002416!7.41e-11!46;UBERON:0003102!5.53e-09!99;UBERON:0005256!1.08e-08!122;UBERON:0000926!1.49e-08!315;UBERON:0004120!1.49e-08!315;UBERON:0006603!1.49e-08!315;UBERON:0002384!2.37e-08!371;UBERON:0002097!2.38e-08!41;UBERON:0005631!3.15e-08!14;UBERON:0000158!3.15e-08!14;UBERON:0004457!8.07e-08!12;UBERON:0000042!8.07e-08!12;UBERON:0004573!2.44e-07!33;UBERON:0004571!2.44e-07!33;UBERON:0001013!2.70e-07!14;UBERON:0001637!4.03e-07!42;UBERON:0003509!4.03e-07!42;UBERON:0004572!4.03e-07!42;UBERON:0003688!6.74e-07!6;UBERON:0002358!6.74e-07!6;UBERON:0003684!6.74e-07!6;UBERON:0001178!6.74e-07!6;UBERON:0002049!6.79e-07!78;UBERON:0007798!6.79e-07!78;UBERON:0003104!6.96e-07!160;UBERON:0009142!6.96e-07!160;UBERON:0004535!9.82e-07!109
|ontology_enrichment_uberon=UBERON:0007524!1.33e-14!73;UBERON:0002329!2.50e-14!71;UBERON:0003059!2.50e-14!71;UBERON:0007282!2.50e-14!71;UBERON:0004290!2.50e-14!71;UBERON:0009618!2.50e-14!71;UBERON:0003077!6.59e-14!72;UBERON:0007285!6.59e-14!72;UBERON:0001134!2.61e-13!62;UBERON:0002036!2.61e-13!62;UBERON:0003082!2.61e-13!62;UBERON:0002385!4.22e-13!64;UBERON:0001015!4.22e-13!64;UBERON:0000383!4.22e-13!64;UBERON:0000486!5.47e-13!83;UBERON:0007503!2.19e-12!78;UBERON:0004923!2.57e-11!66;UBERON:0004872!7.22e-11!83;UBERON:0002199!7.41e-11!46;UBERON:0002416!7.41e-11!46;UBERON:0003102!5.53e-09!99;UBERON:0005256!1.08e-08!122;UBERON:0000926!1.49e-08!315;UBERON:0004120!1.49e-08!315;UBERON:0006603!1.49e-08!315;UBERON:0002384!2.37e-08!371;UBERON:0002097!2.38e-08!41;UBERON:0005631!3.15e-08!14;UBERON:0000158!3.15e-08!14;UBERON:0004457!8.07e-08!12;UBERON:0000042!8.07e-08!12;UBERON:0004573!2.44e-07!33;UBERON:0004571!2.44e-07!33;UBERON:0001013!2.70e-07!14;UBERON:0001637!4.03e-07!42;UBERON:0003509!4.03e-07!42;UBERON:0004572!4.03e-07!42;UBERON:0003688!6.74e-07!6;UBERON:0002358!6.74e-07!6;UBERON:0003684!6.74e-07!6;UBERON:0001178!6.74e-07!6;UBERON:0002049!6.79e-07!78;UBERON:0007798!6.79e-07!78;UBERON:0003104!6.96e-07!160;UBERON:0009142!6.96e-07!160;UBERON:0004535!9.82e-07!109
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}}
}}

Revision as of 14:30, 26 November 2012


Full id: C834_Fibroblast_Sertoli_chorionic_Smooth_Synoviocyte_Preadipocyte_normal



Phase1 CAGE Peaks

Hg19::chr15:48703363..48703377,-p@chr15:48703363..48703377
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Hg19::chr15:48703464..48703484,-p@chr15:48703464..48703484
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Hg19::chr15:48712914..48712923,-p@chr15:48712914..48712923
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Hg19::chr15:48712928..48712948,-p@chr15:48712928..48712948
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Hg19::chr15:48729997..48730011,-p@chr15:48729997..48730011
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Hg19::chr15:48808480..48808519,-p@chr15:48808480..48808519
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Hg19::chr15:48818352..48818368,-p@chr15:48818352..48818368
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Hg19::chr15:48818401..48818413,-p@chr15:48818401..48818413
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Hg19::chr15:48826377..48826399,-p@chr15:48826377..48826399
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Hg19::chr15:48936886..48936898,-p13@FBN1


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
dense mesenchyme tissue1.33e-1473
somite2.50e-1471
presomitic mesoderm2.50e-1471
presumptive segmental plate2.50e-1471
dermomyotome2.50e-1471
trunk paraxial mesoderm2.50e-1471
paraxial mesoderm6.59e-1472
presumptive paraxial mesoderm6.59e-1472
skeletal muscle tissue2.61e-1362
striated muscle tissue2.61e-1362
myotome2.61e-1362
muscle tissue4.22e-1364
musculature4.22e-1364
musculature of body4.22e-1364
multilaminar epithelium5.47e-1383
epithelial vesicle2.19e-1278
organ component layer2.57e-1166
splanchnic layer of lateral plate mesoderm7.22e-1183
integument7.41e-1146
integumental system7.41e-1146
surface structure5.53e-0999
trunk mesenchyme1.08e-08122
mesoderm1.49e-08315
mesoderm-derived structure1.49e-08315
presumptive mesoderm1.49e-08315
connective tissue2.37e-08371
skin of body2.38e-0841
extraembryonic membrane3.15e-0814
membranous layer3.15e-0814
cavity lining8.07e-0812
serous membrane8.07e-0812
systemic artery2.44e-0733
systemic arterial system2.44e-0733
adipose tissue2.70e-0714
artery4.03e-0742
arterial blood vessel4.03e-0742
arterial system4.03e-0742
omentum6.74e-076
peritoneum6.74e-076
abdominal cavity6.74e-076
visceral peritoneum6.74e-076
vasculature6.79e-0778
vascular system6.79e-0778
mesenchyme6.96e-07160
entire embryonic mesenchyme6.96e-07160
cardiovascular system9.82e-07109


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)

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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

No analysis results for this cluster

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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