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Coexpression cluster:C2195: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2195_liposarcoma_Smooth_Fibroblast_CD14_giant_Hepatic_mesothelioma
|full_id=C2195_liposarcoma_Smooth_Fibroblast_CD14_giant_Hepatic_mesothelioma
|id=C2195
|id=C2195

Revision as of 14:53, 12 September 2012


Full id: C2195_liposarcoma_Smooth_Fibroblast_CD14_giant_Hepatic_mesothelioma



Phase1 CAGE Peaks

Hg19::chr12:124873357..124873401,-p1@NCOR2
Hg19::chr12:124873824..124873833,-p19@NCOR2
Hg19::chr12:124873852..124873881,-p3@NCOR2
Hg19::chr12:124873905..124873916,-p@chr12:124873905..124873916
-


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 organism4.67e-17659
anatomical system8.40e-17625
anatomical group1.89e-16626
organism subdivision1.58e-14365
tube2.09e-14194
lateral plate mesoderm2.78e-14216
artery4.24e-1442
arterial blood vessel4.24e-1442
arterial system4.24e-1442
epithelial tube4.62e-14118
mesoderm4.98e-13448
mesoderm-derived structure4.98e-13448
presumptive mesoderm4.98e-13448
organ6.72e-13511
cell layer7.95e-13312
epithelium4.10e-12309
germ layer5.22e-12604
embryonic tissue5.22e-12604
presumptive structure5.22e-12604
epiblast (generic)5.22e-12604
embryonic structure6.50e-12605
developing anatomical structure6.50e-12605
blood vessel1.29e-1160
epithelial tube open at both ends1.29e-1160
blood vasculature1.29e-1160
vascular cord1.29e-1160
systemic artery3.63e-1133
systemic arterial system3.63e-1133
vasculature6.41e-1179
vascular system6.41e-1179
embryo6.57e-11612
anatomical conduit9.26e-11241
splanchnic layer of lateral plate mesoderm1.26e-1084
trunk2.27e-10216
musculoskeletal system2.74e-10167
anatomical cluster8.47e-10286
vessel3.10e-0969
trunk mesenchyme3.44e-09143
dermomyotome3.19e-0870
skeletal muscle tissue4.89e-0861
striated muscle tissue4.89e-0861
myotome4.89e-0861
multi-tissue structure6.55e-08347
muscle tissue6.99e-0863
musculature6.99e-0863
musculature of body6.99e-0863
unilaminar epithelium2.68e-07138
circulatory system4.74e-07113
somite5.20e-0783
paraxial mesoderm5.20e-0783
presomitic mesoderm5.20e-0783
presumptive segmental plate5.20e-0783
trunk paraxial mesoderm5.20e-0783
presumptive paraxial mesoderm5.20e-0783
cardiovascular system8.89e-07110


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#186944.907389214879320.001724022357361790.0106302497922132
ESR1#2099323.07645247211590.0001339105244968570.00175719076114176
TAF1#687243.343046285745290.008005664898701650.0321405257305874



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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