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Coexpression cluster:C1761

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Full id: C1761_Placental_Alveolar_Smooth_Fibroblast_mesothelioma_Renal_Urothelial



Phase1 CAGE Peaks

Hg19::chr16:3070336..3070347,+p2@TNFRSF12A
Hg19::chr16:3070356..3070383,+p1@TNFRSF12A
Hg19::chr16:3071213..3071278,+p@chr16:3071213..3071278
+
Hg19::chr16:3071571..3071641,+p@chr16:3071571..3071641
+
Hg19::chr16:3072067..3072119,-p@chr16:3072067..3072119
-


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><br>


Uber Anatomy
Ontology termp-valuen
trunk mesenchyme5.82e-19143
trunk1.75e-18216
mesenchyme6.66e-16238
entire embryonic mesenchyme6.66e-16238
multilaminar epithelium1.35e-1582
somite2.90e-1483
paraxial mesoderm2.90e-1483
presomitic mesoderm2.90e-1483
presumptive segmental plate2.90e-1483
trunk paraxial mesoderm2.90e-1483
presumptive paraxial mesoderm2.90e-1483
epithelial tube5.47e-14118
multi-cellular organism3.05e-13659
dermomyotome3.41e-1370
unilaminar epithelium3.05e-12138
anatomical system3.23e-12625
anatomical group4.90e-12626
mesoderm1.80e-11448
mesoderm-derived structure1.80e-11448
presumptive mesoderm1.80e-11448
skeletal muscle tissue2.70e-1161
striated muscle tissue2.70e-1161
myotome2.70e-1161
multi-tissue structure5.46e-11347
cell layer5.87e-11312
organism subdivision6.10e-11365
epithelium1.03e-10309
muscle tissue1.11e-1063
musculature1.11e-1063
musculature of body1.11e-1063
vasculature1.29e-1079
vascular system1.29e-1079
artery2.76e-1042
arterial blood vessel2.76e-1042
arterial system2.76e-1042
germ layer2.88e-09604
embryonic tissue2.88e-09604
presumptive structure2.88e-09604
epiblast (generic)2.88e-09604
splanchnic layer of lateral plate mesoderm2.94e-0984
blood vessel3.88e-0960
epithelial tube open at both ends3.88e-0960
blood vasculature3.88e-0960
vascular cord3.88e-0960
embryonic structure4.13e-09605
developing anatomical structure4.13e-09605
embryo5.49e-09612
vessel6.93e-0969
systemic artery1.17e-0833
systemic arterial system1.17e-0833
primordium2.12e-08168
nephron epithelium7.94e-0816
nephron7.94e-0816
uriniferous tubule7.94e-0816
metanephric mesenchyme7.94e-0816
nephrogenic mesenchyme7.94e-0816
ectodermal placode1.04e-0729
subdivision of trunk1.17e-07113
urinary system structure2.30e-0744
excretory tube4.03e-0717
mesonephric epithelium4.03e-0717
mesonephric tubule4.03e-0717
nephric duct4.03e-0717
kidney epithelium4.03e-0717
renal duct4.03e-0717
mesonephric duct4.03e-0717
pronephric duct4.03e-0717
female organism5.63e-0741
renal system6.29e-0745


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
CCNT2#90545.068961261570110.002709998091280770.0148955050079087
EGR1#195843.990543275848110.0067800983001440.0287661149808555
ESR1#2099212.30744131846180.009891532076757460.0371177679852139
ETS1#211347.783008737761870.0005121035947688870.00444031443205212
FOSL1#8061215.88543188654920.006026021505811330.0270050057946977
GABPB1#255345.654147068945740.001776696502096670.0109080245713053
JUNB#3726212.24425306392850.009990490593345960.0374689139612331
SMARCC1#6599326.19801559177890.0001159625626060410.00157633920031398
TAF1#687253.343046285745290.002394600090870310.0135315246667246
ZBTB7A#5134145.881527446300720.001524947561042230.00971477359568683



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.