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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4359_mesenchymal_Mesothelial_Endothelial_Cardiac_mesothelioma_myeloma_anaplastic
|full_id=C4359_mesenchymal_Mesothelial_Endothelial_Cardiac_mesothelioma_myeloma_anaplastic
|id=C4359
|id=C4359

Revision as of 17:25, 12 September 2012


Full id: C4359_mesenchymal_Mesothelial_Endothelial_Cardiac_mesothelioma_myeloma_anaplastic



Phase1 CAGE Peaks

Hg19::chr4:110723252..110723291,-p2@CFI
Hg19::chr4:110723298..110723312,-p3@CFI
Hg19::chr4:110723340..110723356,-p5@CFI


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
endothelial cell of vascular tree2.40e-0824
Uber Anatomy
Ontology termp-valuen
adult organism8.64e-19115
cell layer3.36e-16312
anatomical cluster5.61e-16286
epithelium6.85e-16309
anatomical conduit2.46e-15241
tube1.40e-13194
neural plate1.07e-1286
presumptive neural plate1.07e-1286
neurectoderm2.94e-1190
anatomical system3.42e-11625
anatomical group5.34e-11626
multi-tissue structure1.97e-10347
multi-cellular organism5.18e-10659
central nervous system7.76e-1082
regional part of nervous system2.27e-0994
nervous system2.27e-0994
neural tube1.02e-0857
neural rod1.02e-0857
future spinal cord1.02e-0857
neural keel1.02e-0857
epithelial tube1.67e-08118
regional part of brain2.46e-0859
pre-chordal neural plate2.54e-0861
unilaminar epithelium4.36e-08138
brain4.62e-0869
future brain4.62e-0869
embryo8.54e-08612
embryonic structure9.49e-08605
developing anatomical structure9.49e-08605
compound organ1.34e-0769
organ1.40e-07511
germ layer1.87e-07604
embryonic tissue1.87e-07604
presumptive structure1.87e-07604
epiblast (generic)1.87e-07604
organism subdivision3.78e-07365
primordium7.85e-07168
pigment epithelium of eye8.43e-0711


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
EP300#203336.77394172622320.003216880500103790.0168009092639066
HNF4A#3172323.13229036295378.07584663437677e-050.00123218896515365
SP1#666735.69838137814090.005403962701712170.0247428522842664
STAT3#6774310.51946499715420.0008589184530415310.0064447578358506
TCF7L2#6934310.77017656313730.0008003181298398380.00616086276718087
USF1#739136.361499277207960.00388404057290560.0190891912185265



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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