Coexpression cluster:C441

Full id: C441_keratoacanthoma_skin_tongue_esophagus_cervical_salivary_Sebocyte

Phase1 CAGE Peaks

Hg19::chr10:8636368..8636400,-	p@chr10:8636368..8636400 -
Hg19::chr12:3600112..3600125,+	p6@PRMT8
Hg19::chr14:23777595..23777607,-	p@chr14:23777595..23777607 -
Hg19::chr14:23777630..23777642,-	p@chr14:23777630..23777642 -
Hg19::chr14:23777647..23777667,-	p@chr14:23777647..23777667 -
Hg19::chr16:55600580..55600632,+	p1@CAPNS2
Hg19::chr16:55600644..55600645,+	p2@CAPNS2
Hg19::chr16:80586313..80586337,-	p@chr16:80586313..80586337 -
Hg19::chr17:39672442..39672463,+	p@chr17:39672442..39672463 +
Hg19::chr17:39674844..39674854,+	p@chr17:39674844..39674854 +
Hg19::chr17:40324009..40324020,-	p@chr17:40324009..40324020 -
Hg19::chr1:151826134..151826143,-	p2@THEM5
Hg19::chr1:151826151..151826159,-	p3@THEM5
Hg19::chr1:151826179..151826192,-	p1@THEM5
Hg19::chr1:152572708..152572714,+	p1@LCE3C
Hg19::chr1:236247199..236247215,-	p@chr1:236247199..236247215 -
Hg19::chr20:10727793..10727802,+	p@chr20:10727793..10727802 +
Hg19::chr9:97563025..97563035,+	p@chr9:97563025..97563035 +
Hg19::chr9:97563078..97563086,+	p@chr9:97563078..97563086 +
Hg19::chr9:97563106..97563117,+	p@chr9:97563106..97563117 +
Hg19::chrX:69643154..69643183,+	p1@GDPD2
Hg19::chrX:69643186..69643195,+	p4@GDPD2

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:0035247	peptidyl-arginine omega-N-methylation	0.00691705418196945
GO:0019919	peptidyl-arginine methylation, to asymmetrical-dimethyl arginine	0.00691705418196945
GO:0035246	peptidyl-arginine N-methylation	0.00691705418196945
GO:0035241	protein-arginine omega-N monomethyltransferase activity	0.00691705418196945
GO:0018216	peptidyl-arginine methylation	0.00829997633890119
GO:0008469	histone-arginine N-methyltransferase activity	0.0103731380914246
GO:0016274	protein-arginine N-methyltransferase activity	0.0103731380914246
GO:0016273	arginine N-methyltransferase activity	0.0103731380914246
GO:0018195	peptidyl-arginine modification	0.0124455672994332
GO:0016571	histone methylation	0.0124455672994332
GO:0008889	glycerophosphodiester phosphodiesterase activity	0.0149772478673127
GO:0043393	regulation of protein binding	0.0149772478673127
GO:0008213	protein amino acid alkylation	0.0207279625682647
GO:0006479	protein amino acid methylation	0.0207279625682647
GO:0051098	regulation of binding	0.0257841692883749
GO:0042054	histone methyltransferase activity	0.0275901361221504
GO:0031424	keratinization	0.0275901361221504
GO:0006071	glycerol metabolic process	0.0275901361221504
GO:0019751	polyol metabolic process	0.0275901361221504
GO:0043414	biopolymer methylation	0.0275901361221504
GO:0016570	histone modification	0.0275901361221504
GO:0008276	protein methyltransferase activity	0.0275901361221504
GO:0009913	epidermal cell differentiation	0.0275901361221504
GO:0008170	N-methyltransferase activity	0.0275901361221504
GO:0016569	covalent chromatin modification	0.0275901361221504
GO:0048730	epidermis morphogenesis	0.0291732855349702
GO:0032259	methylation	0.0354271151573729
GO:0048729	tissue morphogenesis	0.0354271151573729
GO:0005886	plasma membrane	0.038525270902211
GO:0008757	S-adenosylmethionine-dependent methyltransferase activity	0.0394621325759638
GO:0046982	protein heterodimerization activity	0.0465741722799623

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
stratified squamous epithelial cell	4.20e-18	6
keratin accumulating cell	4.20e-18	6
stratified epithelial cell	4.20e-18	6
keratinizing barrier epithelial cell	4.20e-18	6
epithelial fate stem cell	4.20e-18	6
stratified epithelial stem cell	4.20e-18	6
surface ectodermal cell	4.20e-18	6
epithelial cell of prostate	2.78e-16	3
buccal mucosa cell	6.82e-13	1
endothelial cell of viscerocranial mucosa	6.82e-13	1
keratinized cell of the oral mucosa	6.82e-13	1
keratinocyte	2.35e-10	5
endo-epithelial cell	7.02e-07	42

Uber Anatomy

Ontology term	p-value	n
surface	2.32e-13	1
mammalian vulva	2.62e-13	1
external female genitalia	2.62e-13	1
tonsil	4.23e-13	1
mucosa-associated lymphoid tissue	4.23e-13	1
lymphoid tissue	4.23e-13	1
tonsillar ring	4.23e-13	1
zone of skin	4.78e-13	4
surface structure	6.17e-13	99
orifice	2.11e-11	36
mouth	4.01e-10	29
stomodeum	4.01e-10	29
oral opening	6.90e-09	22
uterine cervix	8.24e-09	6
neck of organ	8.24e-09	6
skin epidermis	1.14e-07	15
outer epithelium	1.14e-07	15
enveloping layer of ectoderm	1.14e-07	15
open tracheal system trachea	4.98e-07	2

Disease

Ontology term	p-value	n
skin squamous cell carcinoma	1.61e-13	1
keratoacanthoma	1.61e-13	1
skin carcinoma	2.15e-07	2
skin cancer	2.15e-07	2
integumentary system cancer	2.15e-07	2

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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(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
SMC3#9126	5	3.41930291930292	0.0131467926667059	0.0466131816715812

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.