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Coexpression cluster:C3976: Difference between revisions

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|ontology_enrichment_disease=DOID:305!7.14e-09!106;DOID:1749!6.37e-08!14;DOID:14566!3.92e-07!239
|ontology_enrichment_disease=DOID:305!7.14e-09!106;DOID:1749!6.37e-08!14;DOID:14566!3.92e-07!239
|ontology_enrichment_uberon=
|ontology_enrichment_uberon=
|tf_chipseq_enrich=ATF3#467;2:14.9754496840058:0.00576829454079388:0.0259591896214923!FOXA2#3170;2:16.4203091684435:0.00481068235210548:0.0225929874166537!HNF4A#3172;2:15.4215269086358:0.00544421048668661:0.0246761522011571!HNF4G#3174;2:19.1689483509645:0.00354398661128422:0.0179727307806115!POU5F1#5460;1:111.813067150635:0.00891691105511183:0.0338238940066402!SMARCB1#6598;2:12.1684771874383:0.00867500222192174:0.0329937566298356
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}}
}}

Revision as of 14:28, 5 September 2012


Full id: C3976_testicular_extraskeletal_cervical_maxillary_teratocarcinoma_iPS_H9



Phase1 CAGE Peaks

Hg19::chr1:36020462..36020478,-p21@KIAA0319L
Hg19::chr3:99980143..99980163,+p4@TBC1D23
Hg19::chr3:99980167..99980181,+p5@TBC1D23


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


GO IDGO nameFDR corrected p-value
GO:0005097Rab GTPase activator activity0.0239567038401373
GO:0032313regulation of Rab GTPase activity0.0239567038401373
GO:0032482Rab protein signal transduction0.0239567038401373
GO:0032483regulation of Rab protein signal transduction0.0239567038401373
GO:0005099Ras GTPase activator activity0.0239567038401373
GO:0032318regulation of Ras GTPase activity0.0239567038401373
GO:0043087regulation of GTPase activity0.0239567038401373
GO:0051336regulation of hydrolase activity0.0269087147398698
GO:0005096GTPase activator activity0.0269087147398698
GO:0046578regulation of Ras protein signal transduction0.0269087147398698
GO:0007265Ras protein signal transduction0.0269087147398698
GO:0008047enzyme activator activity0.0269087147398698
GO:0005083small GTPase regulator activity0.0269087147398698
GO:0051056regulation of small GTPase mediated signal transduction0.0269087147398698
GO:0050790regulation of catalytic activity0.0320558106676086
GO:0065009regulation of a molecular function0.0327259126893428
GO:0030695GTPase regulator activity0.0327259126893428
GO:0009966regulation of signal transduction0.0353232073472271
GO:0007264small GTPase mediated signal transduction0.0365595196043801



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><br><br>disease_data<br>


Disease
Ontology termp-valuen
carcinoma7.14e-09106
squamous cell carcinoma6.37e-0814
disease of cellular proliferation3.92e-07239


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
ATF3#467214.97544968400580.005768294540793880.0259591896214923
FOXA2#3170216.42030916844350.004810682352105480.0225929874166537
HNF4A#3172215.42152690863580.005444210486686610.0246761522011571
HNF4G#3174219.16894835096450.003543986611284220.0179727307806115
POU5F1#54601111.8130671506350.008916911055111830.0338238940066402
SMARCB1#6598212.16847718743830.008675002221921740.0329937566298356



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.