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Coexpression cluster:C3271: Difference between revisions

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|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189417064082153!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278617403069291!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.032402803295821!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320870928025305!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319442507433633
|tf_chipseq_enrich=CCNT2#905;3:6.33620157696263:0.00393075003576489:0.0189417064082153!CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278617403069291!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.032402803295821!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0320870928025305!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319442507433633
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}}
}}

Revision as of 16:02, 26 November 2012


Full id: C3271_gastric_giant_testicular_pancreatic_ductal_Fibroblast_myxofibrosarcoma



Phase1 CAGE Peaks

Hg19::chr12:26111751..26111762,+p7@RASSF8
Hg19::chr12:26111788..26111811,+p6@RASSF8
Hg19::chr12:26111823..26111862,+p2@RASSF8


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
fibroblast1.09e-1576
vascular associated smooth muscle cell8.61e-0832
non-terminally differentiated cell1.73e-07106
skin fibroblast1.90e-0723
Uber Anatomy
Ontology termp-valuen
multi-cellular organism3.49e-12656
anatomical group4.43e-12625
anatomical system7.49e-12624
anatomical cluster1.90e-11373
multi-tissue structure2.92e-10342
artery1.43e-0942
arterial blood vessel1.43e-0942
arterial system1.43e-0942
systemic artery3.15e-0933
systemic arterial system3.15e-0933
vasculature3.19e-0978
vascular system3.19e-0978
cell layer3.75e-09309
structure with developmental contribution from neural crest4.14e-09132
splanchnic layer of lateral plate mesoderm4.53e-0983
dense mesenchyme tissue6.17e-0973
epithelium6.44e-09306
anatomical conduit7.06e-09240
paraxial mesoderm1.69e-0872
presumptive paraxial mesoderm1.69e-0872
somite1.99e-0871
presomitic mesoderm1.99e-0871
presumptive segmental plate1.99e-0871
dermomyotome1.99e-0871
trunk paraxial mesoderm1.99e-0871
vessel3.26e-0868
epithelial tube open at both ends5.33e-0859
blood vessel5.33e-0859
blood vasculature5.33e-0859
vascular cord5.33e-0859
multilaminar epithelium8.54e-0883
organism subdivision1.92e-07264
tube2.65e-07192
epithelial vesicle6.79e-0778
circulatory system8.64e-07112


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
CCNT2#90536.336201576962630.003930750035764890.0189417064082153
CTCF#1066435.360256373075030.0064925092527670.0278617403069291
E2F1#186934.907389214879320.008460985347239390.032402803295821
E2F6#187635.017155731697390.00791769806886330.0320870928025305
EGR1#195834.988179094810140.008056488137383440.0319442507433633



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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