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Coexpression cluster:C4517: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.03272318355356!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295748760136226
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.03272318355356!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0295748760136226
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}}
}}

Revision as of 16:47, 26 November 2012


Full id: C4517_Smooth_mesenchymal_colon_Meningeal_large_Preadipocyte_Fibroblast



Phase1 CAGE Peaks

Hg19::chr5:72416387..72416409,+p1@TMEM171
Hg19::chr5:72416428..72416441,+p3@TMEM171
Hg19::chr5:72416466..72416490,+p2@TMEM171


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>

Uber Anatomy
Ontology termp-valuen
artery1.28e-2542
arterial blood vessel1.28e-2542
arterial system1.28e-2542
splanchnic layer of lateral plate mesoderm2.99e-2383
epithelial tube open at both ends2.42e-2259
blood vessel2.42e-2259
blood vasculature2.42e-2259
vascular cord2.42e-2259
vasculature9.21e-2278
vascular system9.21e-2278
vessel1.22e-2168
multilaminar epithelium9.72e-2183
systemic artery1.14e-1933
systemic arterial system1.14e-1933
dense mesenchyme tissue1.78e-1973
somite2.88e-1971
presomitic mesoderm2.88e-1971
presumptive segmental plate2.88e-1971
dermomyotome2.88e-1971
trunk paraxial mesoderm2.88e-1971
paraxial mesoderm3.43e-1972
presumptive paraxial mesoderm3.43e-1972
unilaminar epithelium4.01e-19148
epithelial vesicle3.09e-1878
epithelial tube1.79e-17117
cardiovascular system2.00e-15109
skeletal muscle tissue3.49e-1562
striated muscle tissue3.49e-1562
myotome3.49e-1562
muscle tissue4.89e-1564
musculature4.89e-1564
musculature of body4.89e-1564
circulatory system3.41e-14112
cell layer1.53e-13309
trunk mesenchyme1.62e-12122
epithelium1.79e-12306
aorta6.04e-1221
aortic system6.04e-1221
mesenchyme1.22e-10160
entire embryonic mesenchyme1.22e-10160
organism subdivision7.16e-10264
trunk1.05e-09199
anatomical system7.00e-09624
anatomical group9.92e-09625
multi-cellular organism1.93e-08656
anatomical cluster5.38e-08373
blood vessel smooth muscle6.11e-0810
arterial system smooth muscle6.11e-0810
artery smooth muscle tissue6.11e-0810
aorta smooth muscle tissue6.11e-0810
multi-tissue structure6.69e-08342
blood vessel endothelium1.14e-0718
endothelium1.14e-0718
cardiovascular system endothelium1.14e-0718
anatomical conduit2.99e-07240
surface structure4.51e-0799
integument4.82e-0746
integumental system4.82e-0746
organ component layer5.38e-0766
squamous epithelium6.31e-0725
simple squamous epithelium7.24e-0722
skin of body7.40e-0741
smooth muscle tissue8.29e-0715
Disease
Ontology termp-valuen
ovarian cancer8.14e-0714


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
E2F1#186934.907389214879320.008460985347239390.03272318355356
MYC#460935.22228187160940.007020843755740150.0295748760136226



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.

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