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Coexpression cluster:C2294

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Full id: C2294_hepatocellular_small_hepatoblastoma_Hepatocyte_colon_adenocarcinoma_Intestinal



Phase1 CAGE Peaks

Hg19::chr14:39735833..39735859,+p7@CTAGE5
Hg19::chr20:42187542..42187573,-p@chr20:42187542..42187573
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Hg19::chr6:30131199..30131210,-p@chr6:30131199..30131210
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Hg19::chr8:145641934..145641949,-p9@SLC39A4


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


GO IDGO nameFDR corrected p-value
GO:0055038recycling endosome membrane0.0123614848790397
GO:0055037recycling endosome0.0123614848790397
GO:0006829zinc ion transport0.018950649628939
GO:0010008endosome membrane0.0419721296764219
GO:0044440endosomal part0.0419721296764219
GO:0000041transition metal ion transport0.0419721296764219



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
endodermal cell1.07e-0859
epithelial cell5.31e-07254
Disease
Ontology termp-valuen
carcinoma1.29e-09106


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
EP300#203335.08045629466740.01144298405398240.0418787472969781
ESRRA#21011120.9600785340310.008241662461779040.0324811692771978
HEY1#2346244.040111043105710.00375304636917980.0185721113362127
HNF4A#3172211.56614518147680.01057585681762490.0390639048691752
HNF4G#3174321.56506689483510.0001638032421292610.00203587371233343
RXRA#6256210.03730856956660.01391703805920110.0488745935594641
SIN3A#2594245.408884726815140.001168172384885160.00795065204985473
TCF12#693837.975848676639820.003090920396013070.0162748996843564



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.