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Coexpression cluster:C3903: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007524!2.31e-16!73;UBERON:0003077!9.41e-16!72;UBERON:0007285!9.41e-16!72;UBERON:0002329!1.29e-15!71;UBERON:0003059!1.29e-15!71;UBERON:0007282!1.29e-15!71;UBERON:0004290!1.29e-15!71;UBERON:0009618!1.29e-15!71;UBERON:0003102!1.90e-14!99;UBERON:0000486!5.18e-13!83;UBERON:0007503!1.74e-12!78;UBERON:0002199!4.12e-12!46;UBERON:0002416!4.12e-12!46;UBERON:0001134!8.07e-12!62;UBERON:0002036!8.07e-12!62;UBERON:0003082!8.07e-12!62;UBERON:0002385!1.70e-11!64;UBERON:0001015!1.70e-11!64;UBERON:0000383!1.70e-11!64;UBERON:0000479!8.61e-11!773;UBERON:0002097!2.42e-10!41;UBERON:0004872!1.19e-08!83;UBERON:0001637!1.60e-08!42;UBERON:0003509!1.60e-08!42;UBERON:0004572!1.60e-08!42;UBERON:0004573!2.70e-08!33;UBERON:0004571!2.70e-08!33;UBERON:0000468!1.91e-07!656;UBERON:0001013!2.21e-07!14;UBERON:0000475!3.02e-07!264;UBERON:0010314!3.87e-07!132;UBERON:0000481!4.99e-07!342;UBERON:0003104!7.84e-07!160;UBERON:0009142!7.84e-07!160;UBERON:0004237!8.15e-07!10;UBERON:0004695!8.15e-07!10;UBERON:0002111!8.15e-07!10;UBERON:0004178!8.15e-07!10;UBERON:0005256!9.00e-07!122
|ontology_enrichment_uberon=UBERON:0007524!2.31e-16!73;UBERON:0003077!9.41e-16!72;UBERON:0007285!9.41e-16!72;UBERON:0002329!1.29e-15!71;UBERON:0003059!1.29e-15!71;UBERON:0007282!1.29e-15!71;UBERON:0004290!1.29e-15!71;UBERON:0009618!1.29e-15!71;UBERON:0003102!1.90e-14!99;UBERON:0000486!5.18e-13!83;UBERON:0007503!1.74e-12!78;UBERON:0002199!4.12e-12!46;UBERON:0002416!4.12e-12!46;UBERON:0001134!8.07e-12!62;UBERON:0002036!8.07e-12!62;UBERON:0003082!8.07e-12!62;UBERON:0002385!1.70e-11!64;UBERON:0001015!1.70e-11!64;UBERON:0000383!1.70e-11!64;UBERON:0000479!8.61e-11!773;UBERON:0002097!2.42e-10!41;UBERON:0004872!1.19e-08!83;UBERON:0001637!1.60e-08!42;UBERON:0003509!1.60e-08!42;UBERON:0004572!1.60e-08!42;UBERON:0004573!2.70e-08!33;UBERON:0004571!2.70e-08!33;UBERON:0000468!1.91e-07!656;UBERON:0001013!2.21e-07!14;UBERON:0000475!3.02e-07!264;UBERON:0010314!3.87e-07!132;UBERON:0000481!4.99e-07!342;UBERON:0003104!7.84e-07!160;UBERON:0009142!7.84e-07!160;UBERON:0004237!8.15e-07!10;UBERON:0004695!8.15e-07!10;UBERON:0002111!8.15e-07!10;UBERON:0004178!8.15e-07!10;UBERON:0005256!9.00e-07!122
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}}
}}

Revision as of 16:25, 26 November 2012


Full id: C3903_peripheral_splenic_mesenchymal_neuroectodermal_b_dura_Fibroblast



Phase1 CAGE Peaks

Hg19::chr1:170632108..170632114,+p29@PRRX1
Hg19::chr1:170632115..170632136,+p9@PRRX1
Hg19::chr1:170632137..170632172,+p10@PRRX1


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 tissue2.31e-1673
paraxial mesoderm9.41e-1672
presumptive paraxial mesoderm9.41e-1672
somite1.29e-1571
presomitic mesoderm1.29e-1571
presumptive segmental plate1.29e-1571
dermomyotome1.29e-1571
trunk paraxial mesoderm1.29e-1571
surface structure1.90e-1499
multilaminar epithelium5.18e-1383
epithelial vesicle1.74e-1278
integument4.12e-1246
integumental system4.12e-1246
skeletal muscle tissue8.07e-1262
striated muscle tissue8.07e-1262
myotome8.07e-1262
muscle tissue1.70e-1164
musculature1.70e-1164
musculature of body1.70e-1164
tissue8.61e-11773
skin of body2.42e-1041
splanchnic layer of lateral plate mesoderm1.19e-0883
artery1.60e-0842
arterial blood vessel1.60e-0842
arterial system1.60e-0842
systemic artery2.70e-0833
systemic arterial system2.70e-0833
multi-cellular organism1.91e-07656
adipose tissue2.21e-0714
organism subdivision3.02e-07264
structure with developmental contribution from neural crest3.87e-07132
multi-tissue structure4.99e-07342
mesenchyme7.84e-07160
entire embryonic mesenchyme7.84e-07160
blood vessel smooth muscle8.15e-0710
arterial system smooth muscle8.15e-0710
artery smooth muscle tissue8.15e-0710
aorta smooth muscle tissue8.15e-0710
trunk mesenchyme9.00e-07122


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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