Coexpression cluster:C1318

Full id: C1318_retina_Melanocyte_globus_caudate_eye_melanoma_nucleus

Phase1 CAGE Peaks

Hg19::chr10:63123003..63123038,-	p@chr10:63123003..63123038 -
Hg19::chr3:69986115..69986119,+	p12@MITF
Hg19::chr4:22341289..22341308,-	p1@LOC100505912
Hg19::chr6:10412249..10412254,-	p41@TFAP2A
Hg19::chr6:10412262..10412271,-	p21@TFAP2A
Hg19::chr7:116311841..116311852,+	p33@MET

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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p.value	FDR	nGenes	nPathway	Name
1.82684577066052e-05	0.0115639337282811	2	71	Melanoma (KEGG):05218

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:0048012	hepatocyte growth factor receptor signaling pathway	0.00435652890615801
GO:0005008	hepatocyte growth factor receptor activity	0.00435652890615801
GO:0051450	myoblast proliferation	0.00435652890615801
GO:0016563	transcription activator activity	0.00909867646707665
GO:0007275	multicellular organismal development	0.00916255739815988
GO:0030318	melanocyte differentiation	0.014933592894531
GO:0050931	pigment cell differentiation	0.014933592894531
GO:0032502	developmental process	0.0175503814073968
GO:0045178	basal part of cell	0.0175503814073968
GO:0048066	pigmentation during development	0.0175503814073968
GO:0009925	basal plasma membrane	0.0175503814073968
GO:0032501	multicellular organismal process	0.0175503814073968
GO:0030317	sperm motility	0.0195928403967735
GO:0007595	lactation	0.0195928403967735
GO:0003705	RNA polymerase II transcription factor activity, enhancer binding	0.0220380517978679
GO:0030534	adult behavior	0.0220380517978679
GO:0019861	flagellum	0.0257497172747369
GO:0001764	neuron migration	0.0257497172747369
GO:0048513	organ development	0.0257497172747369
GO:0046777	protein amino acid autophosphorylation	0.0285907117347742
GO:0016540	protein autoprocessing	0.0285907117347742
GO:0000187	activation of MAPK activity	0.0331598958932373
GO:0048609	reproductive process in a multicellular organism	0.0331598958932373
GO:0032504	multicellular organism reproduction	0.0331598958932373
GO:0043406	positive regulation of MAP kinase activity	0.0344377311136857
GO:0048731	system development	0.036895850629173
GO:0016323	basolateral plasma membrane	0.0391939630078132
GO:0065007	biological regulation	0.0391939630078132
GO:0043405	regulation of MAP kinase activity	0.0391939630078132
GO:0048869	cellular developmental process	0.0391939630078132
GO:0030154	cell differentiation	0.0391939630078132
GO:0016485	protein processing	0.0403175002874271
GO:0004714	transmembrane receptor protein tyrosine kinase activity	0.0430321421924296
GO:0048856	anatomical structure development	0.0436787634291092
GO:0019199	transmembrane receptor protein kinase activity	0.0443602688604381
GO:0050954	sensory perception of mechanical stimulus	0.0443602688604381
GO:0007605	sensory perception of sound	0.0443602688604381
GO:0007420	brain development	0.0443602688604381
GO:0045860	positive regulation of protein kinase activity	0.0443602688604381
GO:0033674	positive regulation of kinase activity	0.0443602688604381
GO:0043283	biopolymer metabolic process	0.0443602688604381
GO:0007398	ectoderm development	0.0443602688604381
GO:0051347	positive regulation of transferase activity	0.0443602688604381
GO:0000165	MAPKKK cascade	0.0443602688604381
GO:0007517	muscle development	0.0497038261938837

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
neurecto-epithelial cell	4.58e-10	20
columnar/cuboidal epithelial cell	7.05e-10	27
melanocyte	7.52e-09	10
melanoblast	7.52e-09	10
epithelial cell	5.37e-08	254
ecto-epithelial cell	6.98e-08	33

Uber Anatomy

Ontology term	p-value	n
adult organism	8.42e-14	115
neurectoderm	1.97e-12	90
central nervous system	4.86e-12	82
neural tube	8.26e-12	57
neural rod	8.26e-12	57
future spinal cord	8.26e-12	57
neural keel	8.26e-12	57
ectoderm	8.44e-12	173
presumptive ectoderm	8.44e-12	173
brain	1.19e-11	69
future brain	1.19e-11	69
regional part of nervous system	3.64e-11	94
nervous system	3.64e-11	94
regional part of forebrain	9.32e-11	41
forebrain	9.32e-11	41
future forebrain	9.32e-11	41
neural plate	1.30e-10	86
presumptive neural plate	1.30e-10	86
ectoderm-derived structure	2.51e-10	169
anterior neural tube	2.69e-10	42
telencephalon	1.19e-09	34
regional part of telencephalon	2.53e-09	33
regional part of brain	2.55e-09	59
gray matter	5.08e-09	34
brain grey matter	5.08e-09	34
head	6.92e-09	123
anterior region of body	9.96e-09	129
craniocervical region	9.96e-09	129
organ	1.26e-08	511
cerebral hemisphere	2.17e-08	32
pre-chordal neural plate	2.65e-08	61

Disease

Ontology term	p-value	n
cell type cancer	1.20e-09	143
carcinoma	1.86e-07	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.