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Coexpression cluster:C1004

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Full id: C1004_chorionic_pancreatic_choriocarcinoma_amniotic_placenta_colon_Placental



Phase1 CAGE Peaks

Hg19::chr11:7595176..7595189,+p19@PPFIBP2
Hg19::chr17:73982309..73982324,+p4@TEN1
Hg19::chr20:18125679..18125686,+p7@CSRP2BP
Hg19::chr20:18125727..18125755,+p4@CSRP2BP
Hg19::chr20:18125925..18125964,+p5@CSRP2BP
Hg19::chrX:52112136..52112150,+p3@XAGE2B
p3@XAGE2
Hg19::chrX:52112158..52112165,+p1@XAGE2B
p1@XAGE2
Hg19::chrX:52386980..52387013,-p2@XAGE2B
p2@XAGE2


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:0030274LIM domain binding0.0105961823506016
GO:0008907integrase activity0.0150088277864031
GO:0015074DNA integration0.0182422653092127
GO:0008080N-acetyltransferase activity0.0261641131540075
GO:0016407acetyltransferase activity0.0261641131540075
GO:0016410N-acyltransferase activity0.0261641131540075
GO:0019904protein domain specific binding0.0319837703946395
GO:0008415acyltransferase activity0.049075006499733
GO:0016747transferase activity, transferring groups other than amino-acyl groups0.049075006499733



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 cell1.74e-13254
Uber Anatomy
Ontology termp-valuen
extraembryonic membrane4.61e-1214
membranous layer4.61e-1214
chorion1.99e-097
endoderm-derived structure5.48e-07169
endoderm5.48e-07169
presumptive endoderm5.48e-07169
Disease
Ontology termp-valuen
carcinoma7.39e-15106
cell type cancer7.28e-11143
cancer9.46e-07235


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
BHLHE40#8553211.21795338674440.0127147255611290.0458676115809038
HNF4A#317238.674608886107630.003838470874117280.0189392006246485
HNF4G#3174310.78253344741750.002064267375206250.0119712377366409



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.