Personal tools

Coexpression cluster:C4525

From FANTOM5_SSTAR

Revision as of 16:01, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C4525_Fibroblast_Saos2_Chondrocyte_Preadipocyte_Osteoblast_trachea_pleomorphic



Phase1 CAGE Peaks

Hg19::chr5:83016760..83016771,-p4@HAPLN1
Hg19::chr5:83016808..83016832,-p2@HAPLN1
Hg19::chr5:83016840..83016851,-p3@HAPLN1


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>disease_data<br>


Cell Type
Ontology termp-valuen
fibroblast3.48e-1976
non-terminally differentiated cell5.69e-13106
skin fibroblast1.04e-1023
vascular associated smooth muscle cell2.83e-1032
osteoblast2.17e-0911
osteoprogenitor cell2.17e-0911
mesenchyme condensation cell2.17e-0911
Uber Anatomy
Ontology termp-valuen
splanchnic layer of lateral plate mesoderm2.35e-0983
vasculature1.52e-0878
vascular system1.52e-0878
cardiovascular system3.79e-08109
circulatory system4.03e-08112
blood vessel layer1.80e-077
artery2.25e-0742
arterial blood vessel2.25e-0742
arterial system2.25e-0742
skin of body2.67e-0741
epithelial tube open at both ends5.12e-0759
blood vessel5.12e-0759
blood vasculature5.12e-0759
vascular cord5.12e-0759
Disease
Ontology termp-valuen
musculoskeletal system disease1.83e-075
myotonic disease1.83e-075
muscle tissue disease1.83e-075
myopathy1.83e-075
muscular disease1.83e-075
myotonic dystrophy1.83e-075


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.