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Coexpression cluster:C4174: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4174_Endothelial_mesenchymal_epithelioid_Hepatic_migratory_Neural_Mast
|full_id=C4174_Endothelial_mesenchymal_epithelioid_Hepatic_migratory_Neural_Mast
|id=C4174
|id=C4174

Revision as of 17:13, 12 September 2012


Full id: C4174_Endothelial_mesenchymal_epithelioid_Hepatic_migratory_Neural_Mast



Phase1 CAGE Peaks

Hg19::chr2:206547166..206547186,+p2@NRP2
Hg19::chr2:206547199..206547206,+p3@NRP2
Hg19::chr2:206547215..206547232,+p1@NRP2


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
multi-cellular organism2.57e-17659
anatomical system1.38e-16625
anatomical group2.64e-16626
embryo1.93e-13612
embryonic structure6.60e-13605
developing anatomical structure6.60e-13605
germ layer1.36e-12604
embryonic tissue1.36e-12604
presumptive structure1.36e-12604
epiblast (generic)1.36e-12604
vasculature1.59e-1179
vascular system1.59e-1179
vessel2.27e-1069
blood vessel8.81e-0960
epithelial tube open at both ends8.81e-0960
blood vasculature8.81e-0960
vascular cord8.81e-0960
epithelial tube1.76e-08118
organ2.50e-08511
simple squamous epithelium5.96e-0822
epithelium7.04e-08309
cell layer1.36e-07312
endothelium2.04e-0718
blood vessel endothelium2.04e-0718
cardiovascular system endothelium2.04e-0718
lateral plate mesoderm2.79e-07216
mesoderm3.24e-07448
mesoderm-derived structure3.24e-07448
presumptive mesoderm3.24e-07448
anatomical conduit3.28e-07241
tube5.61e-07194
splanchnic layer of lateral plate mesoderm6.08e-0784
squamous epithelium6.80e-0725


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
ESR1#2099330.76860329615453.43136389821584e-050.000678085551874671
MYC#460935.22228187160940.007020843755740150.0295177287953684
NR3C1#2908314.9730233311730.0002978331194675480.00309444818584076
TCF7L2#6934310.77017656313730.0008003181298398380.00615134126893898
ZNF263#1012738.221841637010680.001799043925565870.0109659360652605



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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