Coexpression cluster:C542

Full id: C542_squamous_colon_pharyngeal_ductal_renal_gall_peripheral

Phase1 CAGE Peaks

Hg19::chr14:103560509..103560517,+	p@chr14:103560509..103560517 +
Hg19::chr17:4699695..4699699,-	p@chr17:4699695..4699699 -
Hg19::chr17:47210085..47210098,+	p2@B4GALNT2
Hg19::chr17:47210125..47210136,+	p1@B4GALNT2
Hg19::chr17:76533685..76533690,-	p@chr17:76533685..76533690 -
Hg19::chr20:10619745..10619768,-	p@chr20:10619745..10619768 -
Hg19::chr20:10619777..10619811,-	p@chr20:10619777..10619811 -
Hg19::chr20:10750941..10750951,+	p@chr20:10750941..10750951 +
Hg19::chr2:103353367..103353400,+	p1@TMEM182
Hg19::chr2:165860476..165860511,+	p@chr2:165860476..165860511 +
Hg19::chr2:188385262..188385271,+	p@chr2:188385262..188385271 +
Hg19::chr3:112521361..112521367,+	p1@ENST00000496067
Hg19::chr3:112521387..112521398,+	p2@ENST00000519700
Hg19::chr3:112521422..112521435,+	p1@ENST00000519700
Hg19::chr9:130914175..130914189,+	p@chr9:130914175..130914189 +
Hg19::chr9:130915675..130915689,+	p@chr9:130915675..130915689 +
Hg19::chr9:130915692..130915702,+	p@chr9:130915692..130915702 +

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

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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

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GO ID	GO name	FDR corrected p-value
GO:0019276	UDP-N-acetylgalactosamine metabolic process	0.00735856827869091
GO:0006047	UDP-N-acetylglucosamine metabolic process	0.00735856827869091
GO:0030259	lipid glycosylation	0.00735856827869091
GO:0022408	negative regulation of cell-cell adhesion	0.0103006308464257
GO:0022407	regulation of cell-cell adhesion	0.0103006308464257
GO:0009225	nucleotide-sugar metabolic process	0.0103006308464257
GO:0007162	negative regulation of cell adhesion	0.0154461696665433
GO:0008376	acetylgalactosaminyltransferase activity	0.0154461696665433
GO:0006044	N-acetylglucosamine metabolic process	0.0154461696665433
GO:0006041	glucosamine metabolic process	0.0154461696665433
GO:0006040	amino sugar metabolic process	0.0164477143333733
GO:0030258	lipid modification	0.0191190416765635
GO:0030173	integral to Golgi membrane	0.0205842782151792
GO:0030155	regulation of cell adhesion	0.0205842782151792
GO:0031228	intrinsic to Golgi membrane	0.0205842782151792
GO:0008194	UDP-glycosyltransferase activity	0.0348461799623283
GO:0031301	integral to organelle membrane	0.0348461799623283
GO:0031300	intrinsic to organelle membrane	0.0348461799623283
GO:0005792	microsome	0.0348461799623283
GO:0042598	vesicular fraction	0.0348461799623283
GO:0006486	protein amino acid glycosylation	0.0348461799623283
GO:0043413	biopolymer glycosylation	0.0348461799623283
GO:0009101	glycoprotein biosynthetic process	0.0348461799623283
GO:0009100	glycoprotein metabolic process	0.0381502198512918
GO:0016758	transferase activity, transferring hexosyl groups	0.0494245767274581

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>

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Cell Type

Ontology term	p-value	n
epithelial cell	1.02e-09	254
endo-epithelial cell	1.21e-09	43
endodermal cell	1.21e-08	59

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	1.46e-14	169
endoderm	1.46e-14	169
presumptive endoderm	1.46e-14	169
digestive system	8.69e-13	155
digestive tract	8.69e-13	155
primitive gut	8.69e-13	155
subdivision of digestive tract	4.67e-11	129
endodermal part of digestive tract	4.67e-11	129
endo-epithelium	6.72e-11	82
mixed endoderm/mesoderm-derived structure	5.96e-08	130
epithelial bud	6.04e-08	37
respiratory system	1.36e-07	72
mucosa	2.84e-07	12
gastrointestinal system	3.13e-07	35
hindgut	4.69e-07	19

Disease

Ontology term	p-value	n
cancer	6.38e-21	235
disease of cellular proliferation	1.72e-20	239
carcinoma	4.74e-20	106
cell type cancer	4.18e-19	143
organ system cancer	7.33e-10	137
squamous cell carcinoma	1.08e-07	14

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

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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

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No analysis results for this cluster

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

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This analysis result is provided for C0 - C305 clusters.