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Coexpression cluster:C1339

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Full id: C1339_small_colon_signet_trachea_gall_adenocarcinoma_Renal



Phase1 CAGE Peaks

Hg19::chr11:2925001..2925048,-p4@SLC22A18AS
Hg19::chr3:168991226..168991244,-p@chr3:168991226..168991244
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Hg19::chr6:31846768..31846780,-p1@SLC44A4
Hg19::chr9:130877529..130877536,-p@chr9:130877529..130877536
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Hg19::chr9:130877564..130877577,-p@chr9:130877564..130877577
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Hg19::chr9:130877614..130877619,-p@chr9:130877614..130877619
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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>cell_data<br>uberon_data<br>disease_data<br>


Cell Type
Ontology termp-valuen
endodermal cell2.05e-0959
epithelial cell4.03e-09254
respiratory epithelial cell8.57e-0913
kidney tubule cell1.05e-0712
nephron tubule epithelial cell1.05e-0712
endo-epithelial cell3.43e-0743
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.54e-23169
endoderm1.54e-23169
presumptive endoderm1.54e-23169
subdivision of digestive tract6.41e-23129
endodermal part of digestive tract6.41e-23129
adult organism7.42e-23115
immaterial anatomical entity2.54e-20126
digestive system3.38e-20155
digestive tract3.38e-20155
primitive gut3.38e-20155
trunk region element9.04e-19107
mixed endoderm/mesoderm-derived structure2.49e-18130
endo-epithelium1.04e-1782
anatomical space6.38e-15104
subdivision of trunk2.50e-14113
foregut2.98e-1398
renal system1.60e-1245
urinary system structure7.68e-1244
abdomen element1.08e-1155
abdominal segment element1.08e-1155
multi-tissue structure8.94e-11347
intermediate mesoderm1.57e-1037
organ1.89e-10511
anatomical conduit3.02e-10241
duct4.01e-1026
mesenchyme8.31e-10238
entire embryonic mesenchyme8.31e-10238
abdominal segment of trunk1.55e-0961
abdomen1.55e-0961
thoracic cavity element1.77e-0934
thoracic cavity1.77e-0934
thoracic segment organ5.20e-0935
gut epithelium5.54e-0954
epithelial bud5.61e-0937
embryo7.16e-09612
respiratory tract1.26e-0853
cavitated compound organ1.49e-0832
epithelium of foregut-midgut junction1.88e-0825
anatomical boundary1.88e-0825
hepatobiliary system1.88e-0825
foregut-midgut junction1.88e-0825
septum transversum1.88e-0825
epithelial fold2.59e-0851
sac3.37e-0826
intraembryonic coelom3.40e-0821
urogenital ridge3.74e-0820
mesonephros4.99e-0818
pronephros4.99e-0818
nephrogenic cord4.99e-0818
pronephric mesoderm4.99e-0818
rostral part of nephrogenic cord4.99e-0818
presumptive pronephric mesoderm4.99e-0818
lung7.06e-0822
respiratory tube7.06e-0822
respiration organ7.06e-0822
pair of lungs7.06e-0822
lung primordium7.06e-0822
lung bud7.06e-0822
renal tubule1.05e-0712
nephron tubule1.05e-0712
nephron tubule epithelium1.05e-0712
respiratory system1.05e-0772
multi-cellular organism1.25e-07659
tube1.41e-07194
anatomical cluster2.17e-07286
epithelial sac2.22e-0725
gastrointestinal system2.62e-0735
hindgut2.81e-0719
digestive tract diverticulum2.95e-0723
anatomical cavity2.96e-0770
organ part2.97e-07219
excretory tube3.37e-0717
mesonephric epithelium3.37e-0717
mesonephric tubule3.37e-0717
nephric duct3.37e-0717
kidney epithelium3.37e-0717
renal duct3.37e-0717
mesonephric duct3.37e-0717
pronephric duct3.37e-0717
organism subdivision4.70e-07365
gland4.80e-0759
kidney5.84e-0727
kidney mesenchyme5.84e-0727
kidney rudiment5.84e-0727
kidney field5.84e-0727
epithelium7.98e-07309
embryonic structure8.20e-07605
developing anatomical structure8.20e-07605
Disease
Ontology termp-valuen
carcinoma7.77e-09106


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


No analysis results for this cluster

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.