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Coexpression cluster:C4809

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Full id: C4809_Pericytes_Mesenchymal_Fibroblast_Smooth_Chondrocyte_Preadipocyte_Lens



Phase1 CAGE Peaks

Hg19::chr9:137533542..137533553,+p6@COL5A1
Hg19::chr9:137533569..137533580,+p3@COL5A1
Hg19::chr9:137533862..137533873,+p9@COL5A1


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>


Cell Type
Ontology termp-valuen
fibroblast1.96e-2176
extraembryonic cell3.42e-1119
somatic cell2.75e-10588
non-terminally differentiated cell8.41e-10106
animal cell2.83e-09679
eukaryotic cell2.83e-09679
extracellular matrix secreting cell4.70e-0815
contractile cell5.44e-0859
stromal cell5.53e-0828
preadipocyte7.36e-0812
mesodermal cell8.03e-08121
muscle precursor cell4.36e-0758
myoblast4.36e-0758
multi-potent skeletal muscle stem cell4.36e-0758
multi fate stem cell7.92e-07427
Uber Anatomy
Ontology termp-valuen
extraembryonic structure2.90e-0924
splanchnic layer of lateral plate mesoderm9.44e-0883
extraembryonic membrane1.24e-0714
membranous layer1.24e-0714
vasculature4.72e-0778
vascular system4.72e-0778
vasculature of organ5.09e-0711
epithelial vesicle6.37e-0778


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
SP1#666735.69838137814090.005403962701712170.0248135616884641
ZNF263#1012738.221841637010680.001799043925565870.0110251348751423



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.