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Coexpression cluster:C4309

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Full id: C4309_splenic_tubular_lung_signet_Intestinal_gall_throat



Phase1 CAGE Peaks

Hg19::chr3:185270286..185270303,-p4@LIPH
Hg19::chr3:185270305..185270319,-p5@LIPH
Hg19::chr3:185270325..185270338,-p3@LIPH


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 cell1.58e-08253
Uber Anatomy
Ontology termp-valuen
subdivision of digestive tract7.00e-14118
digestive system1.56e-13145
digestive tract1.56e-13145
primitive gut1.56e-13145
endoderm-derived structure4.71e-13160
endoderm4.71e-13160
presumptive endoderm4.71e-13160
foregut1.31e-0987
respiratory system4.65e-0874
gastrointestinal system4.88e-0825
multi-tissue structure1.52e-07342
endo-epithelium1.56e-0782
respiratory tract3.93e-0754
Disease
Ontology termp-valuen
carcinoma1.09e-17106
cell type cancer3.61e-12143
adenocarcinoma2.89e-0925
squamous cell carcinoma1.24e-0814
cancer4.86e-08235
disease of cellular proliferation1.63e-07239


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
EBF1#187938.9064668465690.00141523283560980.00917647619781787
ELF1#199734.258097958807540.01295179875054610.0463879598665392
FOXA1#3169311.08141974938550.000734755275698670.00582754451994937
GABPB1#255337.067683836182170.002832212825417420.0154566272286027
GATA3#2625327.2365163572064.94721007899563e-050.000852750740122503
GTF2F1#2962312.73966087675770.0004835525047438590.00435022310646429
WRNIP1#568973109.8199643493767.53682839543883e-073.33109953783849e-05



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.