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Coexpression cluster:C3142: Difference between revisions

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|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.032370754219369!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00540676248558725!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00247382785640064
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.032370754219369!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00540676248558725!TFAP2A#7020;3:16.518634373045:0.000221803388076634:0.00247382785640064
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}}
}}

Revision as of 15:57, 26 November 2012


Full id: C3142_Smooth_mesenchymal_small_Sertoli_Lens_Fibroblast_anaplastic



Phase1 CAGE Peaks

Hg19::chr11:32112568..32112575,+p7@RCN1
Hg19::chr11:32112576..32112600,+p3@RCN1
Hg19::chr11:32112612..32112660,+p1@RCN1


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
vasculature1.12e-2078
vascular system1.12e-2078
somite4.20e-1971
presomitic mesoderm4.20e-1971
presumptive segmental plate4.20e-1971
dermomyotome4.20e-1971
trunk paraxial mesoderm4.20e-1971
dense mesenchyme tissue6.57e-1973
unilaminar epithelium1.24e-18148
paraxial mesoderm2.40e-1872
presumptive paraxial mesoderm2.40e-1872
multilaminar epithelium6.64e-1883
epithelial vesicle1.25e-1778
mesenchyme4.59e-17160
entire embryonic mesenchyme4.59e-17160
skeletal muscle tissue1.08e-1662
striated muscle tissue1.08e-1662
myotome1.08e-1662
vessel3.41e-1668
trunk mesenchyme1.25e-15122
muscle tissue1.60e-1564
musculature1.60e-1564
musculature of body1.60e-1564
splanchnic layer of lateral plate mesoderm4.74e-1583
epithelial tube open at both ends7.69e-1459
blood vessel7.69e-1459
blood vasculature7.69e-1459
vascular cord7.69e-1459
cardiovascular system9.42e-14109
organism subdivision3.24e-13264
epithelial tube3.80e-13117
circulatory system1.03e-12112
artery4.39e-1242
arterial blood vessel4.39e-1242
arterial system4.39e-1242
trunk5.71e-12199
cell layer2.88e-11309
epithelium4.05e-11306
systemic artery2.98e-1033
systemic arterial system2.98e-1033
anatomical cluster1.37e-09373
multi-tissue structure1.46e-08342
aorta3.20e-0821
aortic system3.20e-0821
multi-cellular organism1.91e-07656
surface structure8.32e-0799
Disease
Ontology termp-valuen
ovarian cancer1.11e-0814


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#186934.907389214879320.008460985347239390.032370754219369
TAF7#6879311.43306940492390.0006690181981945830.00540676248558725
TFAP2A#7020316.5186343730450.0002218033880766340.00247382785640064



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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