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Coexpression cluster:C4016

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Full id: C4016_gastrointestinal_anaplastic_maxillary_small_smallcell_argyrophil_Bronchial



Phase1 CAGE Peaks

Hg19::chr20:22565370..22565388,-p2@FOXA2
Hg19::chr20:22565612..22565627,-p@chr20:22565612..22565627
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Hg19::chr20:22565646..22565665,-p@chr20:22565646..22565665
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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>


Uber Anatomy
Ontology termp-valuen
endoderm-derived structure4.78e-31169
endoderm4.78e-31169
presumptive endoderm4.78e-31169
digestive system1.91e-29155
digestive tract1.91e-29155
primitive gut1.91e-29155
subdivision of digestive tract2.21e-27129
endodermal part of digestive tract2.21e-27129
endo-epithelium4.19e-2382
mixed endoderm/mesoderm-derived structure1.04e-22130
foregut8.14e-2098
immaterial anatomical entity4.50e-19126
trunk region element9.56e-17107
gut epithelium2.41e-1354
primordium2.46e-13168
thoracic cavity element3.15e-1334
thoracic cavity3.15e-1334
thoracic segment organ1.20e-1235
epithelial bud1.21e-1237
epithelium of foregut-midgut junction1.47e-1225
anatomical boundary1.47e-1225
hepatobiliary system1.47e-1225
foregut-midgut junction1.47e-1225
septum transversum1.47e-1225
lung3.31e-1222
respiratory tube3.31e-1222
respiration organ3.31e-1222
pair of lungs3.31e-1222
lung primordium3.31e-1222
lung bud3.31e-1222
sac6.10e-1226
respiratory tract1.63e-1153
anatomical space1.74e-11104
gastrointestinal system1.87e-1135
epithelial sac2.52e-1125
digestive tract diverticulum9.12e-1123
respiratory system9.45e-1172
intestine2.42e-1027
hepatic diverticulum3.76e-1022
liver primordium3.76e-1022
epithelial fold4.99e-1051
respiratory primordium7.18e-1038
endoderm of foregut7.18e-1038
respiratory tract epithelium1.29e-0919
lung epithelium1.29e-0919
subdivision of trunk1.72e-09113
endocrine system9.14e-0945
mesenchyme1.30e-08238
entire embryonic mesenchyme1.30e-08238
respiratory system epithelium5.04e-0828
liver9.00e-0819
digestive gland9.00e-0819
liver bud9.00e-0819
exocrine gland9.44e-0831
exocrine system9.44e-0831
tracheobronchial tree1.04e-0714
lower respiratory tract1.04e-0714
gland1.31e-0759
multi-tissue structure3.03e-07347
mucosa4.39e-0712
segment of respiratory tract6.93e-0746
Disease
Ontology termp-valuen
carcinoma3.29e-20106
cell type cancer2.39e-14143
cancer3.08e-10235
disease of cellular proliferation1.27e-09239
respiratory system cancer5.02e-0716
squamous cell carcinoma7.98e-0714


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
HDAC2#3066313.41562023662630.0004140761399857210.00391611862573293
SREBF1#6720347.00584944048839.62099323994382e-060.000254768487065541
SUZ12#23512233.41052060737530.00117826764536030.00799955110276175
ZNF263#1012738.221841637010680.001799043925565870.0109563443082497



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.