Personal tools

Coexpression cluster:C1982

From FANTOM5_SSTAR

Revision as of 15:13, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1982_Fibroblast_Mesenchymal_tenocyte_Hair_normal_Synoviocyte_mesenchymal



Phase1 CAGE Peaks

Hg19::chr7:100201080..100201091,+p12@PCOLCE
Hg19::chr7:100201103..100201120,+p3@PCOLCE
Hg19::chr7:100201144..100201162,-p1@ENST00000544873
Hg19::chr7:100202784..100202796,-p@chr7:100202784..100202796
-
Hg19::chr7:100203376..100203387,+p15@PCOLCE


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:0005518collagen binding0.00279642058165548



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
dense mesenchyme tissue1.69e-2173
somite3.08e-2171
presomitic mesoderm3.08e-2171
presumptive segmental plate3.08e-2171
dermomyotome3.08e-2171
trunk paraxial mesoderm3.08e-2171
paraxial mesoderm1.14e-2072
presumptive paraxial mesoderm1.14e-2072
epithelial vesicle1.72e-1878
skeletal muscle tissue4.19e-1862
striated muscle tissue4.19e-1862
myotome4.19e-1862
multilaminar epithelium1.06e-1783
muscle tissue5.09e-1764
musculature5.09e-1764
musculature of body5.09e-1764
trunk mesenchyme4.78e-13122
mesenchyme1.23e-12160
entire embryonic mesenchyme1.23e-12160
integument2.14e-1146
integumental system2.14e-1146
surface structure5.73e-1199
adipose tissue1.67e-0914
skin of body1.70e-0941
unilaminar epithelium4.10e-08148
tissue1.97e-07773
musculoskeletal system2.12e-07167
articulation4.65e-078
skeletal joint4.65e-078
articular system4.65e-078
organism subdivision9.81e-07264


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.