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Coexpression cluster:C1908

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Full id: C1908_smallcell_endometrioid_small_colon_temporal_iPS_duodenum



Phase1 CAGE Peaks

Hg19::chr2:47596641..47596698,+p4@EPCAM
Hg19::chr2:47601035..47601052,+p10@EPCAM
Hg19::chr2:47601065..47601124,+p5@EPCAM
Hg19::chr2:47601125..47601140,+p8@EPCAM
Hg19::chr2:47606991..47607060,+p@chr2:47606991..47607060
+


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>


Cell Type
Ontology termp-valuen
epithelial cell5.71e-16254
endodermal cell7.69e-1159
endo-epithelial cell1.07e-0943
Uber Anatomy
Ontology termp-valuen
adult organism9.22e-15115
regional part of forebrain1.82e-1341
forebrain1.82e-1341
future forebrain1.82e-1341
neural tube5.50e-1357
neural rod5.50e-1357
future spinal cord5.50e-1357
neural keel5.50e-1357
anterior neural tube7.72e-1342
digestive system3.28e-11155
digestive tract3.28e-11155
primitive gut3.28e-11155
gray matter1.05e-1034
brain grey matter1.05e-1034
telencephalon1.27e-1034
pre-chordal neural plate2.25e-1061
cerebral hemisphere2.51e-1032
regional part of telencephalon2.73e-1033
neural plate3.49e-1086
presumptive neural plate3.49e-1086
regional part of brain4.16e-1059
endoderm-derived structure4.39e-10169
endoderm4.39e-10169
presumptive endoderm4.39e-10169
central nervous system7.48e-1082
subdivision of digestive tract9.45e-10129
endodermal part of digestive tract9.45e-10129
multi-tissue structure2.78e-09347
neurectoderm5.53e-0990
gastrointestinal system7.14e-0935
regional part of cerebral cortex1.16e-0822
immaterial anatomical entity1.27e-08126
organ1.39e-08511
anterior region of body1.67e-08129
craniocervical region1.67e-08129
organ part1.92e-08219
ectoderm-derived structure2.91e-08169
head3.52e-08123
regional part of nervous system3.84e-0894
nervous system3.84e-0894
neocortex7.19e-0820
anatomical space9.03e-08104
trunk region element9.20e-08107
brain9.21e-0869
future brain9.21e-0869
endo-epithelium1.10e-0782
ectoderm1.48e-07173
presumptive ectoderm1.48e-07173
cerebral cortex1.91e-0725
pallium1.91e-0725
intestine3.10e-0727
anatomical conduit9.80e-07241
Disease
Ontology termp-valuen
carcinoma1.52e-27106
cell type cancer5.26e-18143
adenocarcinoma1.25e-1325
squamous cell carcinoma9.50e-0914
cancer2.55e-07235
disease of cellular proliferation7.84e-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
CTCF#1066444.288205098460020.005152015588243280.0239398182959841
RAD21#588536.21302033727380.007751055068811640.0318981968764922
SMC3#912639.02695970695970.002650964449467550.0146411462791085



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.