Coexpression cluster:C748

Full id: C748_amniotic_keratoacanthoma_salivary_Keratinocyte_maxillary_Corneal_esophagus

Phase1 CAGE Peaks

Hg19::chr12:52881239..52881250,-	p@chr12:52881239..52881250 -
Hg19::chr18:24129045..24129064,-	p5@KCTD1
Hg19::chr18:24129073..24129122,-	p2@KCTD1
Hg19::chr18:28622699..28622725,-	p1@DSC3
Hg19::chr18:28622729..28622751,-	p2@DSC3
Hg19::chr18:28622774..28622792,-	p3@DSC3
Hg19::chr6:138412531..138412579,-	p@chr6:138412531..138412579 -
Hg19::chr6:138412884..138412951,-	p@chr6:138412884..138412951 -
Hg19::chr6:138417550..138417583,-	p@chr6:138417550..138417583 -
Hg19::chr6:138428549..138428563,-	p1@PERP
Hg19::chr6:138428580..138428599,-	p2@PERP

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:0044459	plasma membrane part	0.0156189599557952
GO:0030054	cell junction	0.0156189599557952
GO:0005886	plasma membrane	0.0309965043918817
GO:0022610	biological adhesion	0.0309965043918817
GO:0007155	cell adhesion	0.0309965043918817

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	1.98e-45	254
endo-epithelial cell	4.33e-17	43
endodermal cell	1.44e-16	59
embryonic cell	4.12e-16	248
squamous epithelial cell	5.96e-11	62
epithelial cell of alimentary canal	1.90e-09	21
ecto-epithelial cell	2.23e-07	33
respiratory epithelial cell	2.32e-07	13

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	9.63e-29	169
endoderm	9.63e-29	169
presumptive endoderm	9.63e-29	169
digestive system	3.23e-22	155
digestive tract	3.23e-22	155
primitive gut	3.23e-22	155
mesenchyme	7.16e-20	238
entire embryonic mesenchyme	7.16e-20	238
subdivision of digestive tract	1.40e-19	129
endodermal part of digestive tract	1.40e-19	129
mixed endoderm/mesoderm-derived structure	4.28e-19	130
multi-tissue structure	1.00e-17	347
respiratory system	2.46e-17	72
foregut	5.24e-15	98
immaterial anatomical entity	1.52e-14	126
anatomical space	2.03e-14	104
trunk	3.15e-14	216
organism subdivision	6.89e-14	365
primordium	8.43e-14	168
multi-cellular organism	1.25e-13	659
respiratory tract	9.46e-13	53
endo-epithelium	5.87e-11	82
orifice	9.59e-11	35
segment of respiratory tract	1.14e-10	46
anatomical system	2.75e-10	625
anatomical group	3.94e-10	626
subdivision of trunk	7.23e-10	113
thoracic segment of trunk	7.34e-10	52
reproductive structure	7.67e-10	59
reproductive system	7.67e-10	59
embryo	8.03e-10	612
organ part	9.81e-10	219
respiratory primordium	1.11e-09	38
endoderm of foregut	1.11e-09	38
female organism	2.00e-09	41
embryonic structure	3.05e-09	605
developing anatomical structure	3.05e-09	605
germ layer	6.03e-09	604
embryonic tissue	6.03e-09	604
presumptive structure	6.03e-09	604
epiblast (generic)	6.03e-09	604
organ segment	1.03e-08	97
trunk region element	1.37e-08	107
epithelial bud	2.04e-08	37
organ	2.64e-08	511
anatomical cluster	2.72e-08	286
cell layer	3.36e-08	312
epithelium	4.16e-08	309
oral opening	5.59e-08	21
thoracic cavity element	6.25e-08	34
thoracic cavity	6.25e-08	34
reproductive organ	6.50e-08	48
anatomical cavity	7.36e-08	70
female reproductive organ	8.21e-08	37
female reproductive system	8.21e-08	37
extraembryonic structure	1.21e-07	24
thoracic segment organ	1.68e-07	35
epithelial fold	1.97e-07	51
extraembryonic membrane	2.23e-07	14
membranous layer	2.23e-07	14
internal genitalia	5.05e-07	25
surface structure	6.10e-07	95
subdivision of head	6.76e-07	48
embryonic uterus	8.60e-07	22

Disease

Ontology term	p-value	n
carcinoma	1.42e-16	106
cell type cancer	1.81e-13	143

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.