Personal tools

Coexpression cluster:C3188

From FANTOM5_SSTAR

Revision as of 14:52, 19 October 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3188_Smooth_Aortic_Alveolar_leiomyoma_iPS_Fibroblast_mesenchymal



Phase1 CAGE Peaks

Hg19::chr11:65623511..65623549,-p3@CFL1
Hg19::chr11:65623641..65623682,-p4@CFL1
Hg19::chr4:10117812..10117828,-p@chr4:10117812..10117828
-


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
mesoderm5.53e-13315
mesoderm-derived structure5.53e-13315
presumptive mesoderm5.53e-13315
epithelial vesicle1.31e-1178
lateral plate mesoderm1.90e-11203
artery4.66e-1142
arterial blood vessel4.66e-1142
arterial system4.66e-1142
epithelial tube open at both ends1.22e-1059
blood vessel1.22e-1059
blood vasculature1.22e-1059
vascular cord1.22e-1059
vessel3.35e-1068
musculoskeletal system3.97e-10167
vasculature4.66e-1078
vascular system4.66e-1078
dense mesenchyme tissue1.96e-0973
somite2.54e-0971
presomitic mesoderm2.54e-0971
presumptive segmental plate2.54e-0971
dermomyotome2.54e-0971
trunk paraxial mesoderm2.54e-0971
paraxial mesoderm3.97e-0972
presumptive paraxial mesoderm3.97e-0972
splanchnic layer of lateral plate mesoderm9.08e-0983
epithelial tube1.46e-08117
cardiovascular system2.27e-08109
multilaminar epithelium3.51e-0883
circulatory system4.73e-08112
unilaminar epithelium7.98e-08148
systemic artery1.52e-0733
systemic arterial system1.52e-0733
skeletal muscle tissue5.81e-0762
striated muscle tissue5.81e-0762
myotome5.81e-0762
trunk mesenchyme9.27e-07122


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.