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Coexpression cluster:C2376

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Full id: C2376_esophagus_amniotic_throat_tonsil_tongue_salivary_endometrioid



Phase1 CAGE Peaks

Hg19::chr16:4940321..4940338,-p@chr16:4940321..4940338
-
Hg19::chr16:4987129..4987156,-p1@PPL
Hg19::chr16:4987174..4987185,-p3@PPL
Hg19::chr16:4987202..4987221,-p2@PPL


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 cell4.30e-28254
endo-epithelial cell1.58e-1543
endodermal cell8.29e-1459
epithelial cell of alimentary canal8.48e-0921
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.27e-23169
endoderm2.27e-23169
presumptive endoderm2.27e-23169
digestive system8.83e-20155
digestive tract8.83e-20155
primitive gut8.83e-20155
multi-tissue structure8.75e-19347
organ2.54e-17511
subdivision of digestive tract1.62e-16129
endodermal part of digestive tract1.62e-16129
respiratory system4.18e-1672
organ part1.10e-15219
mixed endoderm/mesoderm-derived structure2.65e-15130
multi-cellular organism2.42e-14659
immaterial anatomical entity2.73e-13126
primordium7.12e-13168
foregut7.97e-1398
anatomical space8.47e-13104
organism subdivision7.96e-12365
embryo2.87e-11612
anatomical system1.03e-10625
respiratory tract1.10e-1053
anatomical group1.69e-10626
trunk region element3.39e-10107
endo-epithelium1.14e-0982
embryonic structure1.63e-09605
developing anatomical structure1.63e-09605
epithelial fold2.32e-0951
thoracic segment organ2.50e-0935
germ layer3.57e-09604
embryonic tissue3.57e-09604
presumptive structure3.57e-09604
epiblast (generic)3.57e-09604
thoracic cavity element3.93e-0934
thoracic cavity3.93e-0934
mesenchyme4.86e-09238
entire embryonic mesenchyme4.86e-09238
orifice5.62e-0935
respiratory primordium8.42e-0938
endoderm of foregut8.42e-0938
adult organism8.90e-09115
oral opening1.57e-0821
epithelium2.02e-08309
segment of respiratory tract2.36e-0846
cell layer3.28e-08312
epithelial bud1.67e-0737
ectoderm-derived structure3.78e-07169
organ segment3.78e-0797
reproductive structure4.91e-0759
reproductive system4.91e-0759
subdivision of head6.67e-0748
gland7.24e-0759
anatomical cluster8.33e-07286
Disease
Ontology termp-valuen
carcinoma1.39e-18106
cell type cancer5.70e-12143
squamous cell carcinoma8.35e-0714
adenocarcinoma9.05e-0725


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
ESR1#2099323.07645247211590.0001339105244968570.0017576324328173
HNF4A#3172317.34921777221530.0003125641557482750.00321487963976699
HNF4G#3174321.56506689483510.0001638032421292610.00203611602055913
ZBTB7A#5134135.513931980906920.009038352821081090.0342348141399517



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.