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Coexpression cluster:C2788: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00819187957473469!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106724658277819!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323031965520033
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00819187957473469!E2F1#1869;4:4.90738921487932:0.00172402235736179:0.0106724658277819!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323031965520033
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}}
}}

Revision as of 15:43, 26 November 2012


Full id: C2788_Urothelial_Fibroblast_Small_Smooth_Mallassezderived_Myoblast_Gingival



Phase1 CAGE Peaks

Hg19::chr4:177713756..177713777,-p4@VEGFC
Hg19::chr4:177713788..177713805,-p6@VEGFC
Hg19::chr4:177714068..177714085,-p1@VEGFC
Hg19::chr4:177714098..177714111,-p3@VEGFC


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
multilaminar epithelium2.27e-2183
organism subdivision2.15e-20264
epithelial vesicle2.60e-1978
somite5.55e-1871
presomitic mesoderm5.55e-1871
presumptive segmental plate5.55e-1871
dermomyotome5.55e-1871
trunk paraxial mesoderm5.55e-1871
paraxial mesoderm1.32e-1772
presumptive paraxial mesoderm1.32e-1772
dense mesenchyme tissue1.63e-1773
surface structure3.41e-1799
trunk6.69e-16199
trunk mesenchyme9.21e-16122
skeletal muscle tissue6.18e-1562
striated muscle tissue6.18e-1562
myotome6.18e-1562
unilaminar epithelium1.18e-14148
muscle tissue1.62e-1464
musculature1.62e-1464
musculature of body1.62e-1464
artery5.11e-1442
arterial blood vessel5.11e-1442
arterial system5.11e-1442
mesenchyme1.25e-13160
entire embryonic mesenchyme1.25e-13160
multi-tissue structure2.17e-13342
epithelium3.62e-13306
cell layer4.19e-13309
splanchnic layer of lateral plate mesoderm5.33e-1383
epithelial tube open at both ends7.31e-1359
blood vessel7.31e-1359
blood vasculature7.31e-1359
vascular cord7.31e-1359
vessel8.59e-1368
multi-cellular organism2.81e-12656
vasculature5.69e-1278
vascular system5.69e-1278
systemic artery2.00e-1133
systemic arterial system2.00e-1133
anatomical system2.79e-11624
epithelial tube4.48e-11117
anatomical group4.67e-11625
integument1.16e-0946
integumental system1.16e-0946
anatomical cluster1.23e-09373
skin of body6.90e-0941
anatomical conduit1.55e-08240
cardiovascular system1.46e-07109
circulatory system1.56e-07112
Disease
Ontology termp-valuen
ovarian cancer2.00e-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
CTCF#1066445.360256373075030.001211145381643620.00819187957473469
E2F1#186944.907389214879320.001724022357361790.0106724658277819
TAF1#687243.343046285745290.008005664898701650.0323031965520033



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.