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Coexpression cluster:C907: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;8:4.3621237465594:2.18983367577486e-05:0.000481077070391777!POLR2A#5430;8:1.90884726805162:0.011661228959883:0.0425834647322104!STAT1#6772;3:6.90219583239973:0.00759156108216665:0.0312886759218786
|tf_chipseq_enrich=E2F1#1869;8:4.3621237465594:2.18983367577486e-05:0.000481077070391777!POLR2A#5430;8:1.90884726805162:0.011661228959883:0.0425834647322104!STAT1#6772;3:6.90219583239973:0.00759156108216665:0.0312886759218786
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}}
}}

Revision as of 14:33, 26 November 2012


Full id: C907_Adipocyte_aorta_Smooth_Hepatic_Fibroblast_spleen_Mesenchymal



Phase1 CAGE Peaks

Hg19::chr14:92413867..92413880,-p11@FBLN5
Hg19::chr14:92413889..92413894,-p19@FBLN5
Hg19::chr14:92413896..92413917,-p10@FBLN5
Hg19::chr14:92413918..92413933,-p5@FBLN5
Hg19::chr14:92413955..92413970,-p6@FBLN5
Hg19::chr14:92413978..92413995,-p8@FBLN5
Hg19::chr14:92413998..92414054,-p3@FBLN5
Hg19::chr14:92414055..92414065,-p15@FBLN5
Hg19::chr14:92414271..92414293,-p21@FBLN5


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
fibroblast2.68e-1876
muscle precursor cell4.62e-1158
myoblast4.62e-1158
multi-potent skeletal muscle stem cell4.62e-1158
fat cell1.62e-1015
muscle cell8.05e-1055
contractile cell1.14e-0959
electrically responsive cell2.64e-0861
electrically active cell2.64e-0861
smooth muscle cell5.40e-0843
smooth muscle myoblast5.40e-0843
preadipocyte7.38e-0812
skin fibroblast9.85e-0723
Uber Anatomy
Ontology termp-valuen
adult organism2.18e-17114
muscle tissue1.62e-1364
musculature1.62e-1364
musculature of body1.62e-1364
dense mesenchyme tissue2.48e-1373
paraxial mesoderm4.03e-1372
presumptive paraxial mesoderm4.03e-1372
somite5.27e-1371
presomitic mesoderm5.27e-1371
presumptive segmental plate5.27e-1371
dermomyotome5.27e-1371
trunk paraxial mesoderm5.27e-1371
multi-tissue structure7.12e-13342
skeletal muscle tissue1.16e-1262
striated muscle tissue1.16e-1262
myotome1.16e-1262
tissue1.58e-10773
epithelial vesicle1.77e-1078
multi-cellular organism1.20e-09656
trunk mesenchyme1.39e-09122
multilaminar epithelium1.41e-0983
organism subdivision3.24e-09264
mesenchyme4.10e-09160
entire embryonic mesenchyme4.10e-09160
adipose tissue1.54e-0814
primary circulatory organ1.04e-0727
trunk2.33e-07199
anatomical cluster2.50e-07373
cell layer6.25e-07309
anatomical system7.25e-07624
anatomical group9.56e-07625


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)

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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
E2F1#186984.36212374655942.18983367577486e-050.000481077070391777
POLR2A#543081.908847268051620.0116612289598830.0425834647322104
STAT1#677236.902195832399730.007591561082166650.0312886759218786



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.