Coexpression cluster:C594

Full id: C594_Keratinocyte_Placental_amniotic_Esophageal_tongue_Corneal_Prostate

Phase1 CAGE Peaks

Hg19::chr12:52867616..52867640,-	p2@KRT6C
Hg19::chr12:52881014..52881084,-	p@chr12:52881014..52881084 -
Hg19::chr12:52881094..52881129,-	p@chr12:52881094..52881129 -
Hg19::chr12:52881151..52881162,-	p@chr12:52881151..52881162 -
Hg19::chr12:52881340..52881386,-	p@chr12:52881340..52881386 -
Hg19::chr12:52881401..52881421,-	p@chr12:52881401..52881421 -
Hg19::chr12:52881422..52881438,-	p@chr12:52881422..52881438 -
Hg19::chr12:52881440..52881469,-	p@chr12:52881440..52881469 -
Hg19::chr12:52881475..52881528,-	p@chr12:52881475..52881528 -
Hg19::chr12:52884399..52884420,-	p7@KRT6A
Hg19::chr12:52885340..52885349,-	p10@KRT6A
Hg19::chr12:52885355..52885376,-	p2@KRT6A
Hg19::chr12:52886485..52886506,-	p6@KRT6A
Hg19::chr12:52886515..52886548,-	p4@KRT6A
Hg19::chr12:52887034..52887049,-	p1@KRT6A

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:0045111	intermediate filament cytoskeleton	0.00086501357605482
GO:0005882	intermediate filament	0.00086501357605482
GO:0044430	cytoskeletal part	0.00875313881962261
GO:0005856	cytoskeleton	0.0156475434545066
GO:0005200	structural constituent of cytoskeleton	0.0359851262584485
GO:0043232	intracellular non-membrane-bound organelle	0.037983235872607
GO:0043228	non-membrane-bound organelle	0.037983235872607
GO:0007398	ectoderm development	0.0385963645451909
GO:0008284	positive regulation of cell proliferation	0.0483587763804884
GO:0044446	intracellular organelle part	0.0483587763804884
GO:0044422	organelle part	0.0483587763804884

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
endo-epithelial cell	2.57e-19	43
epithelial cell	1.23e-12	254
endodermal cell	1.86e-12	59
epithelial cell of alimentary canal	2.96e-10	21
respiratory epithelial cell	2.39e-09	13
general ecto-epithelial cell	1.09e-07	13

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	9.54e-17	169
endoderm	9.54e-17	169
presumptive endoderm	9.54e-17	169
respiratory system	3.34e-14	72
respiratory tract	8.53e-11	53
digestive system	1.21e-10	155
digestive tract	1.21e-10	155
primitive gut	1.21e-10	155
mixed endoderm/mesoderm-derived structure	1.63e-10	130
orifice	1.83e-10	35
extraembryonic membrane	5.11e-10	14
membranous layer	5.11e-10	14
organ component layer	1.81e-09	57
surface structure	9.47e-09	95
endo-epithelium	2.28e-08	82
subdivision of digestive tract	2.78e-08	129
endodermal part of digestive tract	2.78e-08	129
organ part	3.84e-08	219
thoracic segment organ	4.24e-08	35
chorion	5.38e-08	7
pharynx	5.87e-08	11
thoracic cavity element	1.10e-07	34
thoracic cavity	1.10e-07	34
neck	1.12e-07	10
embryo	1.64e-07	612
epithelial fold	1.87e-07	51
embryonic structure	2.14e-07	605
developing anatomical structure	2.14e-07	605
chordate pharynx	2.31e-07	10
pharyngeal region of foregut	2.31e-07	10
organ	3.02e-07	511
oral opening	3.09e-07	21
segment of respiratory tract	3.38e-07	46
tracheobronchial tree	3.65e-07	14
lower respiratory tract	3.65e-07	14
epithelial bud	4.45e-07	37
respiratory system epithelium	4.67e-07	28
germ layer	4.72e-07	604
embryonic tissue	4.72e-07	604
presumptive structure	4.72e-07	604
epiblast (generic)	4.72e-07	604

Disease

Ontology term	p-value	n
squamous cell carcinoma	2.54e-08	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.