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Coexpression cluster:C1898

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Full id: C1898_oral_lung_pharyngeal_bronchial_pleomorphic_squamous_Urothelial



Phase1 CAGE Peaks

Hg19::chr2:234600297..234600308,+p4@UGT1A6
Hg19::chr2:234600310..234600325,+p3@UGT1A6
Hg19::chr2:234600339..234600365,+p1@UGT1A6
Hg19::chr2:234600370..234600381,+p5@UGT1A6
Hg19::chr2:234602089..234602097,+p11@UGT1A6


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 structure3.07e-22169
endoderm3.07e-22169
presumptive endoderm3.07e-22169
respiratory system9.55e-2072
digestive system8.96e-17155
digestive tract8.96e-17155
primitive gut8.96e-17155
respiratory tract3.18e-1553
mixed endoderm/mesoderm-derived structure9.72e-15130
subdivision of digestive tract1.29e-14129
endodermal part of digestive tract1.29e-14129
orifice5.17e-1335
foregut8.15e-1198
epithelial bud2.02e-1037
respiratory primordium2.41e-1038
endoderm of foregut2.41e-1038
segment of respiratory tract2.93e-1046
endo-epithelium3.49e-1082
renal system1.56e-0845
oral opening1.96e-0821
thoracic cavity element2.31e-0834
thoracic cavity2.31e-0834
urinary system structure5.44e-0844
thoracic segment organ5.91e-0835
anatomical space1.01e-07104
urothelium1.86e-075
thoracic segment of trunk2.90e-0752
mucosa2.99e-0712
epithelial fold3.12e-0751
Disease
Ontology termp-valuen
carcinoma2.65e-19106
squamous cell carcinoma1.86e-1314
cell type cancer1.20e-12143
adenocarcinoma5.15e-0925


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
STAT3#677448.415571997723390.0003771527211598630.00374353288777941



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.