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Coexpression cluster:C2490: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000475!2.50e-14!264;UBERON:0000481!6.62e-14!342;UBERON:0003102!1.48e-13!99;UBERON:0003104!2.54e-13!160;UBERON:0009142!2.54e-13!160;UBERON:0000119!7.54e-13!309;UBERON:0000468!2.81e-12!656;UBERON:0000483!3.70e-12!306;UBERON:0007503!3.98e-12!78;UBERON:0000486!1.58e-11!83;UBERON:0000490!1.99e-11!148;UBERON:0005256!4.32e-11!122;UBERON:0007524!5.79e-11!73;UBERON:0002329!9.18e-11!71;UBERON:0003059!9.18e-11!71;UBERON:0007282!9.18e-11!71;UBERON:0004290!9.18e-11!71;UBERON:0009618!9.18e-11!71;UBERON:0000477!1.05e-10!373;UBERON:0003077!1.24e-10!72;UBERON:0007285!1.24e-10!72;UBERON:0000467!3.77e-10!624;UBERON:0001637!3.85e-10!42;UBERON:0003509!3.85e-10!42;UBERON:0004572!3.85e-10!42;UBERON:0000480!6.17e-10!625;UBERON:0002100!1.24e-09!199;UBERON:0003914!4.54e-09!117;UBERON:0002049!6.53e-09!78;UBERON:0007798!6.53e-09!78;UBERON:0004872!1.19e-08!83;UBERON:0002097!1.22e-08!41;UBERON:0002199!1.38e-08!46;UBERON:0002416!1.38e-08!46;UBERON:0001134!1.59e-08!62;UBERON:0002036!1.59e-08!62;UBERON:0003082!1.59e-08!62;UBERON:0002385!1.63e-08!64;UBERON:0001015!1.63e-08!64;UBERON:0000383!1.63e-08!64;UBERON:0007500!5.03e-08!59;UBERON:0001981!5.03e-08!59;UBERON:0004537!5.03e-08!59;UBERON:0006965!5.03e-08!59;UBERON:0004573!1.95e-07!33;UBERON:0004571!1.95e-07!33;UBERON:0000055!2.44e-07!68;UBERON:0004923!3.44e-07!66
|ontology_enrichment_uberon=UBERON:0000475!2.50e-14!264;UBERON:0000481!6.62e-14!342;UBERON:0003102!1.48e-13!99;UBERON:0003104!2.54e-13!160;UBERON:0009142!2.54e-13!160;UBERON:0000119!7.54e-13!309;UBERON:0000468!2.81e-12!656;UBERON:0000483!3.70e-12!306;UBERON:0007503!3.98e-12!78;UBERON:0000486!1.58e-11!83;UBERON:0000490!1.99e-11!148;UBERON:0005256!4.32e-11!122;UBERON:0007524!5.79e-11!73;UBERON:0002329!9.18e-11!71;UBERON:0003059!9.18e-11!71;UBERON:0007282!9.18e-11!71;UBERON:0004290!9.18e-11!71;UBERON:0009618!9.18e-11!71;UBERON:0000477!1.05e-10!373;UBERON:0003077!1.24e-10!72;UBERON:0007285!1.24e-10!72;UBERON:0000467!3.77e-10!624;UBERON:0001637!3.85e-10!42;UBERON:0003509!3.85e-10!42;UBERON:0004572!3.85e-10!42;UBERON:0000480!6.17e-10!625;UBERON:0002100!1.24e-09!199;UBERON:0003914!4.54e-09!117;UBERON:0002049!6.53e-09!78;UBERON:0007798!6.53e-09!78;UBERON:0004872!1.19e-08!83;UBERON:0002097!1.22e-08!41;UBERON:0002199!1.38e-08!46;UBERON:0002416!1.38e-08!46;UBERON:0001134!1.59e-08!62;UBERON:0002036!1.59e-08!62;UBERON:0003082!1.59e-08!62;UBERON:0002385!1.63e-08!64;UBERON:0001015!1.63e-08!64;UBERON:0000383!1.63e-08!64;UBERON:0007500!5.03e-08!59;UBERON:0001981!5.03e-08!59;UBERON:0004537!5.03e-08!59;UBERON:0006965!5.03e-08!59;UBERON:0004573!1.95e-07!33;UBERON:0004571!1.95e-07!33;UBERON:0000055!2.44e-07!68;UBERON:0004923!3.44e-07!66
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}}
}}

Revision as of 15:32, 26 November 2012


Full id: C2490_Olfactory_mesothelioma_Hair_leiomyoma_mesenchymal_papillary_tenocyte



Phase1 CAGE Peaks

Hg19::chr19:41765476..41765492,+p@chr19:41765476..41765492
+
Hg19::chr19:41765598..41765618,+p5@AXL
Hg19::chr19:41765634..41765656,+p7@AXL
Hg19::chr19:41765859..41765888,+p6@AXL


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
organism subdivision2.50e-14264
multi-tissue structure6.62e-14342
surface structure1.48e-1399
mesenchyme2.54e-13160
entire embryonic mesenchyme2.54e-13160
cell layer7.54e-13309
multi-cellular organism2.81e-12656
epithelium3.70e-12306
epithelial vesicle3.98e-1278
multilaminar epithelium1.58e-1183
unilaminar epithelium1.99e-11148
trunk mesenchyme4.32e-11122
dense mesenchyme tissue5.79e-1173
somite9.18e-1171
presomitic mesoderm9.18e-1171
presumptive segmental plate9.18e-1171
dermomyotome9.18e-1171
trunk paraxial mesoderm9.18e-1171
anatomical cluster1.05e-10373
paraxial mesoderm1.24e-1072
presumptive paraxial mesoderm1.24e-1072
anatomical system3.77e-10624
artery3.85e-1042
arterial blood vessel3.85e-1042
arterial system3.85e-1042
anatomical group6.17e-10625
trunk1.24e-09199
epithelial tube4.54e-09117
vasculature6.53e-0978
vascular system6.53e-0978
splanchnic layer of lateral plate mesoderm1.19e-0883
skin of body1.22e-0841
integument1.38e-0846
integumental system1.38e-0846
skeletal muscle tissue1.59e-0862
striated muscle tissue1.59e-0862
myotome1.59e-0862
muscle tissue1.63e-0864
musculature1.63e-0864
musculature of body1.63e-0864
epithelial tube open at both ends5.03e-0859
blood vessel5.03e-0859
blood vasculature5.03e-0859
vascular cord5.03e-0859
systemic artery1.95e-0733
systemic arterial system1.95e-0733
vessel2.44e-0768
organ component layer3.44e-0766


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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