Coexpression cluster:C683

Full id: C683_esophagus_tongue_tonsil_Corneal_cervical_Esophageal_throat

Phase1 CAGE Peaks

Hg19::chr11:119039032..119039058,+	p5@NLRX1
Hg19::chr11:119039069..119039081,+	p9@NLRX1
Hg19::chr14:24732368..24732391,-	p1@TGM1
Hg19::chr14:24732403..24732410,-	p4@TGM1
Hg19::chr14:24732738..24732753,-	p3@TGM1
Hg19::chr1:153285441..153285450,-	p@chr1:153285441..153285450 -
Hg19::chr1:24645832..24645853,+	p1@GRHL3
Hg19::chr1:24645865..24645871,+	p6@GRHL3
Hg19::chr1:24645921..24645973,+	p2@GRHL3
Hg19::chr20:33880168..33880183,-	p2@FAM83C
Hg19::chr6:53794788..53794806,+	p12@MLIP
Hg19::chr7:44029862..44029900,-	p1@ENST00000420754

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:0043163	cell envelope organization and biogenesis	0.0157183645563999
GO:0005913	cell-cell adherens junction	0.0336544548770559
GO:0003810	protein-glutamine gamma-glutamyltransferase activity	0.0336544548770559
GO:0001533	cornified envelope	0.0336544548770559
GO:0045229	external encapsulating structure organization and biogenesis	0.0336544548770559
GO:0018149	peptide cross-linking	0.0336544548770559
GO:0030216	keratinocyte differentiation	0.0336544548770559
GO:0031424	keratinization	0.0357618532746787
GO:0016755	transferase activity, transferring amino-acyl groups	0.0357618532746787
GO:0009913	epidermal cell differentiation	0.0359650815239245
GO:0005912	adherens junction	0.0359650815239245
GO:0048730	epidermis morphogenesis	0.0359650815239245
GO:0048729	tissue morphogenesis	0.0434381461036677

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	1.29e-18	254
endo-epithelial cell	6.23e-15	43
endodermal cell	2.84e-11	59
respiratory epithelial cell	2.33e-08	13
epithelial cell of alimentary canal	1.04e-07	21

Uber Anatomy

Ontology term	p-value	n
endoderm-derived structure	4.18e-12	169
endoderm	4.18e-12	169
presumptive endoderm	4.18e-12	169
organ part	1.55e-10	219
organ	6.88e-10	511
anatomical space	1.29e-09	104
respiratory system	1.51e-09	72
digestive system	3.41e-08	155
digestive tract	3.41e-08	155
primitive gut	3.41e-08	155
mixed endoderm/mesoderm-derived structure	8.03e-08	130
immaterial anatomical entity	8.29e-08	126
orifice	9.65e-08	35
subdivision of digestive tract	1.15e-07	129
endodermal part of digestive tract	1.15e-07	129
adult organism	1.16e-07	115
multi-cellular organism	1.83e-07	659
embryo	3.29e-07	612
trunk region element	4.33e-07	107
organism subdivision	4.64e-07	365
renal system	5.25e-07	45
oral opening	6.18e-07	21

Disease

Ontology term	p-value	n
carcinoma	4.17e-08	106
squamous cell carcinoma	1.47e-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)
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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
MAFK#7975	3	6.77518328445748	0.00860006079038526	0.0327624201673188

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.