Coexpression cluster:C3356

Full id: C3356_Urothelial_cervical_tongue_Neutrophils_keratoacanthoma_uterus_Sebocyte

Phase1 CAGE Peaks

Hg19::chr13:20806422..20806431,-	p5@GJB6
Hg19::chr13:20806445..20806465,-	p1@GJB6
Hg19::chr1:17575584..17575598,+	p1@PADI3

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:0000052	citrulline metabolic process	0.00953614299461548
GO:0019240	citrulline biosynthetic process	0.00953614299461548
GO:0018101	peptidyl-citrulline biosynthetic process from peptidyl-arginine	0.00953614299461548
GO:0004668	protein-arginine deiminase activity	0.00953614299461548
GO:0018195	peptidyl-arginine modification	0.00953614299461548
GO:0019794	nonprotein amino acid metabolic process	0.0123607570157109
GO:0016813	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines	0.0158907641848528
GO:0005922	connexon complex	0.0163691689000625
GO:0042471	ear morphogenesis	0.0163691689000625
GO:0000051	urea cycle intermediate metabolic process	0.0163691689000625
GO:0005921	gap junction	0.0163691689000625
GO:0048839	inner ear development	0.0167693862056444
GO:0043583	ear development	0.017107839654105
GO:0014704	intercalated disc	0.0177757148183469
GO:0016324	apical plasma membrane	0.0239960942437855
GO:0045177	apical part of cell	0.0267705471660034
GO:0007423	sensory organ development	0.0267705471660034
GO:0048598	embryonic morphogenesis	0.0273384166545695
GO:0018193	peptidyl-amino acid modification	0.0332405229851315
GO:0050954	sensory perception of mechanical stimulus	0.0332405229851315
GO:0007605	sensory perception of sound	0.0332405229851315
GO:0044271	nitrogen compound biosynthetic process	0.0353274091037163
GO:0005911	intercellular junction	0.0397528999299051
GO:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	0.0409514170360427
GO:0008285	negative regulation of cell proliferation	0.0475291114397334
GO:0009790	embryonic development	0.0477251786241198

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	2.23e-16	42
respiratory epithelial cell	2.06e-11	13
endodermal cell	9.10e-11	58
transitional epithelial cell	2.61e-08	4
urothelial cell	2.61e-08	4

Uber Anatomy

Ontology term	p-value	n
neural tube	1.31e-21	56
neural rod	1.31e-21	56
future spinal cord	1.31e-21	56
neural keel	1.31e-21	56
regional part of nervous system	1.61e-18	53
regional part of brain	1.61e-18	53
ecto-epithelium	7.28e-18	104
regional part of cerebral cortex	3.40e-17	22
central nervous system	3.95e-17	81
adult organism	1.24e-16	114
regional part of forebrain	2.97e-16	41
forebrain	2.97e-16	41
anterior neural tube	2.97e-16	41
future forebrain	2.97e-16	41
telencephalon	4.69e-16	34
brain grey matter	5.24e-16	34
gray matter	5.24e-16	34
cerebral hemisphere	6.61e-16	32
regional part of telencephalon	8.61e-16	32
ectoderm-derived structure	2.67e-15	171
ectoderm	2.67e-15	171
presumptive ectoderm	2.67e-15	171
organ system subdivision	4.39e-15	223
neocortex	6.92e-15	20
cerebral cortex	1.36e-14	25
pallium	1.36e-14	25
brain	1.68e-14	68
future brain	1.68e-14	68
nervous system	2.48e-14	89
neural plate	1.13e-13	82
presumptive neural plate	1.13e-13	82
neurectoderm	1.41e-12	86
pre-chordal neural plate	1.15e-10	61
urothelium	1.47e-09	5
structure with developmental contribution from neural crest	3.95e-09	132
orifice	1.79e-08	36
endoderm-derived structure	7.52e-08	160
endoderm	7.52e-08	160
presumptive endoderm	7.52e-08	160
transitional epithelium	7.81e-08	6
organ part	1.48e-07	218

Disease

Ontology term	p-value	n
squamous cell carcinoma	3.55e-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)
{{{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.