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Coexpression cluster:C4158: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4158_Smooth_Mesenchymal_Cardiac_Nucleus_extraskeletal_mucinous_Lymphatic
|full_id=C4158_Smooth_Mesenchymal_Cardiac_Nucleus_extraskeletal_mucinous_Lymphatic
|id=C4158
|id=C4158

Revision as of 17:12, 12 September 2012


Full id: C4158_Smooth_Mesenchymal_Cardiac_Nucleus_extraskeletal_mucinous_Lymphatic



Phase1 CAGE Peaks

Hg19::chr2:188330292..188330295,-p5@TFPI
Hg19::chr2:188330646..188330688,-p4@TFPI
Hg19::chr2:188330885..188330910,-p6@TFPI


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
unilaminar epithelium2.16e-22138
trunk mesenchyme2.44e-18143
epithelial tube8.91e-18118
trunk2.36e-16216
mesenchyme3.86e-16238
entire embryonic mesenchyme3.86e-16238
mesoderm2.89e-15448
mesoderm-derived structure2.89e-15448
presumptive mesoderm2.89e-15448
vasculature6.22e-1479
vascular system6.22e-1479
splanchnic layer of lateral plate mesoderm1.35e-1384
muscle tissue6.84e-1363
musculature6.84e-1363
musculature of body6.84e-1363
skeletal muscle tissue2.38e-1261
striated muscle tissue2.38e-1261
myotome2.38e-1261
multi-tissue structure4.95e-12347
dermomyotome6.06e-1270
cardiovascular system1.14e-11110
vessel1.58e-1169
somite1.93e-1183
paraxial mesoderm1.93e-1183
presomitic mesoderm1.93e-1183
presumptive segmental plate1.93e-1183
trunk paraxial mesoderm1.93e-1183
presumptive paraxial mesoderm1.93e-1183
circulatory system2.33e-11113
multi-cellular organism2.60e-11659
blood vessel2.30e-1060
epithelial tube open at both ends2.30e-1060
blood vasculature2.30e-1060
vascular cord2.30e-1060
multilaminar epithelium2.88e-1082
anatomical cluster3.33e-10286
cell layer9.07e-09312
epithelium1.56e-08309
embryo3.72e-08612
anatomical system3.91e-08625
anatomical group6.09e-08626
embryonic structure7.05e-08605
developing anatomical structure7.05e-08605
artery9.39e-0842
arterial blood vessel9.39e-0842
arterial system9.39e-0842
digestive system1.01e-07155
digestive tract1.01e-07155
primitive gut1.01e-07155
germ layer1.04e-07604
embryonic tissue1.04e-07604
presumptive structure1.04e-07604
epiblast (generic)1.04e-07604
gut epithelium2.97e-0754
endoderm-derived structure4.68e-07169
endoderm4.68e-07169
presumptive endoderm4.68e-07169
primordium8.21e-07168
subdivision of digestive tract9.09e-07129
endodermal part of digestive tract9.09e-07129


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.