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Coexpression cluster:C3717

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Full id: C3717_cervical_bronchogenic_glassy_epitheloid_Hep2_small_adenocarcinoma



Phase1 CAGE Peaks

Hg19::chr18:33767302..33767315,-p3@uc002kzp.2
Hg19::chr18:33767331..33767359,-p2@uc002kzp.2
Hg19::chr21:44842602..44842620,-p@chr21:44842602..44842620
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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
epithelial cell3.29e-14253
epithelial cell of gall bladder8.64e-072
Uber Anatomy
Ontology termp-valuen
larynx4.13e-289
respiratory primordium2.58e-2238
endoderm of foregut2.58e-2238
digestive system4.02e-19145
digestive tract4.02e-19145
primitive gut4.02e-19145
endoderm-derived structure7.75e-19160
endoderm7.75e-19160
presumptive endoderm7.75e-19160
subdivision of digestive tract5.25e-18118
respiratory tract4.49e-1654
foregut1.58e-1587
segment of respiratory tract4.46e-1547
respiratory system3.63e-1374
upper respiratory tract2.61e-1219
endo-epithelium1.45e-0982
gallbladder1.91e-093
gall bladder primordium1.91e-093
trunk region element1.69e-07101
primordium4.22e-07160
Disease
Ontology termp-valuen
carcinoma1.94e-30106
cell type cancer1.73e-24143
cancer2.31e-15235
disease of cellular proliferation8.17e-15239
lung cancer5.55e-0715


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
PRDM1#639287.88730385164050.0001716248848029080.00209152057688809
TFAP2A#7020211.01242291536330.01054990655215560.039010823197868
ZEB1#6935211.25895467836260.01010222676646330.0378119363961817



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.