Personal tools

Coexpression cluster:C3604

From FANTOM5_SSTAR

Revision as of 19:18, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3604_Mesenchymal_Alveolar_Renal_Hair_Fibroblast_Hepatic_Smooth



Phase1 CAGE Peaks

Hg19::chr17:1389027..1389094,-p1@MYO1C
Hg19::chr17:1394912..1394935,-p4@MYO1C
Hg19::chr17:1394940..1394987,-p2@MYO1C


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
trunk4.46e-24216
trunk mesenchyme5.48e-22143
mesenchyme1.65e-21238
entire embryonic mesenchyme1.65e-21238
somite1.36e-1783
paraxial mesoderm1.36e-1783
presomitic mesoderm1.36e-1783
presumptive segmental plate1.36e-1783
trunk paraxial mesoderm1.36e-1783
presumptive paraxial mesoderm1.36e-1783
multilaminar epithelium1.53e-1782
organism subdivision1.46e-16365
surface structure5.03e-1695
dermomyotome7.45e-1670
epithelial tube1.81e-15118
multi-tissue structure5.03e-14347
muscle tissue1.14e-1363
musculature1.14e-1363
musculature of body1.14e-1363
skeletal muscle tissue1.86e-1361
striated muscle tissue1.86e-1361
myotome1.86e-1361
unilaminar epithelium9.21e-13138
splanchnic layer of lateral plate mesoderm1.71e-1284
vasculature4.41e-1179
vascular system4.41e-1179
integument7.30e-1145
integumental system7.30e-1145
blood vessel1.19e-1060
epithelial tube open at both ends1.19e-1060
blood vasculature1.19e-1060
vascular cord1.19e-1060
skin of body1.61e-1040
multi-cellular organism2.28e-10659
vessel2.29e-1069
subdivision of trunk5.93e-10113
mesoderm1.07e-09448
mesoderm-derived structure1.07e-09448
presumptive mesoderm1.07e-09448
artery1.09e-0942
arterial blood vessel1.09e-0942
arterial system1.09e-0942
cell layer1.77e-09312
epithelium2.40e-09309
anatomical system1.72e-08625
endoderm-derived structure2.07e-08169
endoderm2.07e-08169
presumptive endoderm2.07e-08169
anatomical group2.24e-08626
compound organ6.64e-0869
systemic artery1.10e-0733
systemic arterial system1.10e-0733
circulatory system1.31e-07113
immaterial anatomical entity2.67e-07126
cardiovascular system2.74e-07110
anatomical space4.84e-07104
primordium6.31e-07168


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


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.