Coexpression cluster:C3310

Full id: C3310_Keratinocyte_Bronchial_Corneal_Small_Tracheal_Mammary_Prostate

Phase1 CAGE Peaks

Hg19::chr12:58159332..58159353,-	p3@CYP27B1
Hg19::chr12:58159361..58159394,-	p2@CYP27B1
Hg19::chr17:28898830..28898835,-	p1@ENST00000420566

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:0004498	calcidiol 1-monooxygenase activity	0.00167785234899329
GO:0016709	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen	0.0212527964205816
GO:0009110	vitamin biosynthetic process	0.0212527964205816
GO:0019825	oxygen binding	0.0218120805369128
GO:0006766	vitamin metabolic process	0.0218120805369128
GO:0006874	cellular calcium ion homeostasis	0.0218120805369128
GO:0055074	calcium ion homeostasis	0.0218120805369128
GO:0006875	cellular metal ion homeostasis	0.0218120805369128
GO:0055065	metal ion homeostasis	0.0218120805369128
GO:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	0.0218120805369128
GO:0030005	cellular di-, tri-valent inorganic cation homeostasis	0.0218120805369128
GO:0055066	di-, tri-valent inorganic cation homeostasis	0.0218120805369128
GO:0006816	calcium ion transport	0.0218120805369128
GO:0030003	cellular cation homeostasis	0.0218120805369128
GO:0055080	cation homeostasis	0.0218120805369128
GO:0004497	monooxygenase activity	0.0218120805369128
GO:0055082	cellular chemical homeostasis	0.0218120805369128
GO:0006873	cellular ion homeostasis	0.0218120805369128
GO:0015674	di-, tri-valent inorganic cation transport	0.0218120805369128
GO:0050801	ion homeostasis	0.0220309308433032
GO:0020037	heme binding	0.0220309308433032
GO:0046906	tetrapyrrole binding	0.0220309308433032
GO:0048878	chemical homeostasis	0.0220309308433032
GO:0019725	cellular homeostasis	0.0262164429530201
GO:0042592	homeostatic process	0.0322147651006711
GO:0005506	iron ion binding	0.0324599896747548
GO:0030001	metal ion transport	0.0423813074819786
GO:0006118	electron transport	0.0434443911792905
GO:0006812	cation transport	0.0491205739412173
GO:0006091	generation of precursor metabolites and energy	0.0499685402684563
GO:0006629	lipid metabolic process	0.0499685402684563
GO:0065008	regulation of biological quality	0.0499685402684563

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	9.39e-23	254
endo-epithelial cell	6.61e-16	43
endodermal cell	6.70e-13	59
respiratory epithelial cell	4.69e-10	13
epithelial cell of alimentary canal	1.42e-08	21
general ecto-epithelial cell	5.65e-08	13

Uber Anatomy

Ontology term	p-value	n
respiratory system	1.00e-17	72
endoderm-derived structure	3.22e-16	169
endoderm	3.22e-16	169
presumptive endoderm	3.22e-16	169
respiratory tract	7.10e-14	53
upper respiratory tract	6.24e-12	19
segment of respiratory tract	1.69e-11	46
digestive system	2.52e-11	155
digestive tract	2.52e-11	155
primitive gut	2.52e-11	155
mixed endoderm/mesoderm-derived structure	1.47e-10	130
foregut	2.43e-09	98
larynx	2.52e-09	9
subdivision of digestive tract	1.13e-08	129
endodermal part of digestive tract	1.13e-08	129
orifice	1.60e-08	35
oral opening	1.95e-08	21
respiratory primordium	3.68e-08	38
endoderm of foregut	3.68e-08	38
mouth	8.13e-07	28
stomodeum	8.13e-07	28

Disease

Ontology term	p-value	n
squamous cell carcinoma	6.70e-10	14
carcinoma	3.65e-09	106

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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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.