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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2948_rhabdomyosarcoma_rectum_Saos2_teratocarcinoma_cerebellum_mesothelioma_gastrointestinal
|full_id=C2948_rhabdomyosarcoma_rectum_Saos2_teratocarcinoma_cerebellum_mesothelioma_gastrointestinal
|id=C2948
|id=C2948

Revision as of 15:45, 12 September 2012


Full id: C2948_rhabdomyosarcoma_rectum_Saos2_teratocarcinoma_cerebellum_mesothelioma_gastrointestinal



Phase1 CAGE Peaks

Hg19::chr9:98258815..98258820,-p@chr9:98258815..98258820
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Hg19::chr9:98271426..98271454,-p3@PTCH1
Hg19::chr9:98271460..98271496,-p@chr9:98271460..98271496
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Hg19::chr9:98271524..98271555,-p@chr9:98271524..98271555
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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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism6.83e-26115
central nervous system2.56e-2582
regional part of nervous system3.11e-2594
nervous system3.11e-2594
neural tube1.95e-2157
neural rod1.95e-2157
future spinal cord1.95e-2157
neural keel1.95e-2157
brain8.00e-2069
future brain8.00e-2069
neurectoderm4.09e-1890
regional part of brain4.57e-1859
neural plate9.14e-1786
presumptive neural plate9.14e-1786
regional part of forebrain2.45e-1641
forebrain2.45e-1641
future forebrain2.45e-1641
gray matter3.96e-1634
brain grey matter3.96e-1634
anterior neural tube6.46e-1642
telencephalon9.04e-1634
regional part of telencephalon1.94e-1533
cerebral hemisphere5.48e-1532
ectoderm3.64e-14173
presumptive ectoderm3.64e-14173
ectoderm-derived structure4.55e-13169
cerebral cortex2.46e-1225
pallium2.46e-1225
pre-chordal neural plate4.47e-1261
regional part of cerebral cortex8.66e-1222
head9.70e-12123
anterior region of body1.21e-11129
craniocervical region1.21e-11129
neocortex5.95e-1120
multi-tissue structure1.20e-07347
organ part3.84e-07219
posterior neural tube9.13e-0715
chordal neural plate9.13e-0715


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
BATF#10538318.26835134422770.0002681660105721290.00286868687679428
FOSL2#2355312.69765045342130.000787568572975710.00616958252272803
FOXA1#316938.311064812039090.002740138182109850.0150421703864058
FOXA2#3170318.47284781449890.0002594484187437260.00278255631599671
IRF4#3662316.43588451505810.0003669431395554610.00366098343064891
MEF2A#4205314.0574231822330.0005830038854186610.00489023715277805
PAX5#507935.002174148383370.01196533174786410.0435295834755182
RFX5#599339.035933120396320.002144561191324070.0123914703325419
SMARCB1#6598313.68953683586810.0006305783409379340.00518354752847043
USF1#739134.771124457905970.01370465887188020.0483449593974293
USF2#739239.74414803880220.001718341848410070.0107282343559361



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.