Personal tools

Coexpression cluster:C4191

From FANTOM5_SSTAR

Revision as of 14:22, 21 June 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C4191_Smooth_Mesenchymal_leiomyoma_Fibroblast_Preadipocyte_Adipocyte_Placental



Phase1 CAGE Peaks

Hg19::chr2:220408260..220408340,-p2@CHPF
Hg19::chr2:220408430..220408555,-p1@CHPF
Hg19::chr9:139981401..139981451,+p1@MAN1B1


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

GO IDGO nameFDR corrected p-value
GO:0050510N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity0.00718206835348578
GO:0047238glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity0.00718206835348578
GO:0009311oligosaccharide metabolic process0.0157036058276523
GO:0004571mannosyl-oligosaccharide 1,2-alpha-mannosidase activity0.0157036058276523
GO:0015924mannosyl-oligosaccharide mannosidase activity0.0157036058276523
GO:0008376acetylgalactosaminyltransferase activity0.0157036058276523
GO:0015020glucuronosyltransferase activity0.0157036058276523
GO:0015923mannosidase activity0.0157036058276523
GO:0006487protein amino acid N-linked glycosylation0.0211319491565653
GO:0008194UDP-glycosyltransferase activity0.0486020383091593
GO:0006486protein amino acid glycosylation0.0486020383091593
GO:0043413biopolymer glycosylation0.0486020383091593
GO:0009101glycoprotein biosynthetic process0.0486020383091593
GO:0004553hydrolase activity, hydrolyzing O-glycosyl compounds0.0486020383091593
GO:0009100glycoprotein metabolic process0.0492197354072614
GO:0016798hydrolase activity, acting on glycosyl bonds0.0492197354072614



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 subdivision7.07e-23365
trunk1.88e-17216
multi-tissue structure1.26e-15347
trunk mesenchyme6.64e-14143
multilaminar epithelium3.16e-1382
mesenchyme1.81e-12238
entire embryonic mesenchyme1.81e-12238
skeletal muscle tissue8.34e-1261
striated muscle tissue8.34e-1261
myotome8.34e-1261
somite1.06e-1183
paraxial mesoderm1.06e-1183
presomitic mesoderm1.06e-1183
presumptive segmental plate1.06e-1183
trunk paraxial mesoderm1.06e-1183
presumptive paraxial mesoderm1.06e-1183
dermomyotome2.91e-1170
muscle tissue5.17e-1163
musculature5.17e-1163
musculature of body5.17e-1163
cell layer1.40e-10312
epithelium1.92e-10309
primordium2.29e-10168
subdivision of trunk2.92e-08113
multi-cellular organism3.18e-08659
immaterial anatomical entity6.07e-08126
organ component layer6.34e-0857
extraembryonic membrane4.47e-0714
membranous layer4.47e-0714
extraembryonic structure5.70e-0724
organ part6.86e-07219
ectodermal placode7.67e-0729


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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C4191&oldid=1834094"