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Coexpression cluster:C3925: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3925_Mast_testicular_breast_choriocarcinoma_Mesenchymal_gastrointestinal_smallcell
|full_id=C3925_Mast_testicular_breast_choriocarcinoma_Mesenchymal_gastrointestinal_smallcell
|id=C3925
|id=C3925

Revision as of 16:55, 12 September 2012


Full id: C3925_Mast_testicular_breast_choriocarcinoma_Mesenchymal_gastrointestinal_smallcell



Phase1 CAGE Peaks

Hg19::chr1:204042233..204042249,+p1@SOX13
Hg19::chr1:204042275..204042286,+p4@SOX13
Hg19::chr1:204042723..204042784,+p3@SOX13


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
adult organism2.99e-19115
multi-cellular organism3.14e-19659
anatomical conduit5.01e-18241
anatomical system2.05e-15625
anatomical group4.40e-15626
tube3.44e-14194
anatomical cluster3.93e-14286
embryo4.58e-13612
epithelium5.26e-13309
organ part5.63e-13219
subdivision of digestive tract1.86e-12129
endodermal part of digestive tract1.86e-12129
cell layer1.99e-12312
organ2.91e-12511
endoderm-derived structure4.76e-12169
endoderm4.76e-12169
presumptive endoderm4.76e-12169
digestive system3.06e-11155
digestive tract3.06e-11155
primitive gut3.06e-11155
embryonic structure4.83e-11605
developing anatomical structure4.83e-11605
immaterial anatomical entity5.01e-11126
organism subdivision5.59e-11365
germ layer9.80e-11604
embryonic tissue9.80e-11604
presumptive structure9.80e-11604
epiblast (generic)9.80e-11604
mixed endoderm/mesoderm-derived structure1.04e-10130
multi-tissue structure1.22e-09347
foregut1.73e-0998
neural tube1.98e-0957
neural rod1.98e-0957
future spinal cord1.98e-0957
neural keel1.98e-0957
trunk region element7.86e-09107
central nervous system2.33e-0882
anatomical space4.34e-08104
subdivision of trunk6.42e-08113
primordium1.43e-07168
endothelium2.19e-0718
blood vessel endothelium2.19e-0718
cardiovascular system endothelium2.19e-0718
brain4.19e-0769
future brain4.19e-0769
ectoderm-derived structure4.50e-07169
neural plate5.91e-0786
presumptive neural plate5.91e-0786
regional part of brain6.96e-0759
regional part of nervous system7.40e-0794
nervous system7.40e-0794
Disease
Ontology termp-valuen
carcinoma6.34e-16106
cell type cancer3.58e-10143


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#1066435.360256373075030.0064925092527670.0279593919614767
NR2C2#7182221.74307393682720.002762207975496010.0151386565256522
SMC3#9126210.02995522995520.0126656379767470.0457537464858871
ZNF263#1012738.221841637010680.001799043925565870.0109486829754778



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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