Coexpression cluster:C610

Full id: C610_melanoma_Melanocyte_migratory_mycosis_cerebellum_epithelioid_retina

Phase1 CAGE Peaks

Hg19::chr10:101825164..101825200,-	p3@CPN1
Hg19::chr10:29811555..29811564,-	p35@SVIL
Hg19::chr10:29811606..29811631,-	p15@SVIL
Hg19::chr10:29811632..29811647,-	p20@SVIL
Hg19::chr10:29811664..29811673,-	p33@SVIL
Hg19::chr1:236046697..236046708,-	p15@LYST
Hg19::chr1:236046717..236046726,-	p17@LYST
Hg19::chr1:236046729..236046740,-	p11@LYST
Hg19::chr1:236046799..236046806,-	p18@LYST
Hg19::chr1:236046834..236046841,-	p22@LYST
Hg19::chr1:236046843..236046855,-	p8@LYST
Hg19::chr1:236046879..236046882,-	p24@LYST
Hg19::chr1:236046891..236046902,-	p12@LYST
Hg19::chr2:106227025..106227040,-	p1@LOC285000

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:0004184	lysine carboxypeptidase activity	0.0190717246048572
GO:0043034	costamere	0.0190717246048572
GO:0008333	endosome to lysosome transport	0.0190717246048572
GO:0007041	lysosomal transport	0.0223363955704967
GO:0051693	actin filament capping	0.0223363955704967
GO:0051016	barbed-end actin filament capping	0.0223363955704967
GO:0030835	negative regulation of actin filament depolymerization	0.0223363955704967
GO:0030834	regulation of actin filament depolymerization	0.0223363955704967
GO:0030042	actin filament depolymerization	0.0223363955704967
GO:0007034	vacuolar transport	0.0223363955704967
GO:0051015	actin filament binding	0.0223363955704967
GO:0016197	endosome transport	0.0223363955704967
GO:0004182	carboxypeptidase A activity	0.0223363955704967
GO:0008064	regulation of actin polymerization and/or depolymerization	0.0223363955704967
GO:0051261	protein depolymerization	0.0223363955704967
GO:0030832	regulation of actin filament length	0.0223363955704967
GO:0032535	regulation of cellular component size	0.0223363955704967
GO:0032956	regulation of actin cytoskeleton organization and biogenesis	0.0223363955704967
GO:0004181	metallocarboxypeptidase activity	0.0223363955704967
GO:0051129	negative regulation of cellular component organization and biogenesis	0.0223363955704967
GO:0030016	myofibril	0.0223363955704967
GO:0051493	regulation of cytoskeleton organization and biogenesis	0.0223363955704967
GO:0033043	regulation of organelle organization and biogenesis	0.0223363955704967
GO:0005856	cytoskeleton	0.0223363955704967
GO:0044449	contractile fiber part	0.0223363955704967
GO:0008154	actin polymerization and/or depolymerization	0.0223363955704967
GO:0043292	contractile fiber	0.022564953280771
GO:0007519	skeletal muscle development	0.0227770052946295
GO:0006968	cellular defense response	0.0231581945711703
GO:0004180	carboxypeptidase activity	0.0231581945711703
GO:0014706	striated muscle development	0.0270042522324104
GO:0051128	regulation of cellular component organization and biogenesis	0.0297171835320079
GO:0051248	negative regulation of protein metabolic process	0.0299657971946987
GO:0008235	metalloexopeptidase activity	0.0327074740495181
GO:0007517	muscle development	0.0466333195564237
GO:0008238	exopeptidase activity	0.0492700420420545
GO:0005768	endosome	0.0494677962577345

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><br>

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Cell Type

Ontology term	p-value	n
neurecto-epithelial cell	3.38e-09	20
melanocyte	9.54e-08	10
melanoblast	9.54e-08	10
conventional dendritic cell	2.39e-07	8
columnar/cuboidal epithelial cell	2.47e-07	27
pigment cell	4.91e-07	14

Uber Anatomy

Ontology term	p-value	n
adult organism	8.35e-23	115
neural tube	7.80e-15	57
neural rod	7.80e-15	57
future spinal cord	7.80e-15	57
neural keel	7.80e-15	57
regional part of brain	1.73e-13	59
neural plate	4.87e-13	86
presumptive neural plate	4.87e-13	86
brain	8.48e-13	69
future brain	8.48e-13	69
neurectoderm	1.62e-12	90
central nervous system	2.29e-12	82
regional part of nervous system	2.81e-12	94
nervous system	2.81e-12	94
head	1.32e-09	123
anterior region of body	1.52e-09	129
craniocervical region	1.52e-09	129
posterior neural tube	5.88e-09	15
chordal neural plate	5.88e-09	15
pre-chordal neural plate	2.73e-08	61
anterior neural tube	3.00e-08	42
regional part of forebrain	8.69e-08	41
forebrain	8.69e-08	41
future forebrain	8.69e-08	41
ectoderm-derived structure	1.24e-07	169
segmental subdivision of nervous system	1.49e-07	13
ectoderm	1.75e-07	173
presumptive ectoderm	1.75e-07	173
gray matter	2.34e-07	34
brain grey matter	2.34e-07	34
telencephalon	2.79e-07	34
regional part of telencephalon	8.33e-07	33
segmental subdivision of hindbrain	8.39e-07	12
hindbrain	8.39e-07	12
presumptive hindbrain	8.39e-07	12

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
BATF#10538	5	8.69921492582273	0.000170731701412579	0.0020828230538288
EP300#2033	8	3.87082384355611	0.000292351760388241	0.0031023090330408
JUND#3727	8	3.9969508239263	0.000232670106061253	0.00255653163671028
MEF2A#4205	5	6.69401103915859	0.000575616867065241	0.00485910523597047
PAX5#5079	8	3.81118030353019	0.000326413374511703	0.0033288044547044
STAT3#6774	8	6.01112285551671	1.1795981756812e-05	0.000298729519568304
TFAP2A#7020	8	9.43921964173997	3.88124860065147e-07	1.88888034763951e-05
USF1#7391	8	3.63514244411883	0.000455878887848724	0.00423627859845475
USF2#7392	8	7.42411279146834	2.41644431268328e-06	8.54915405055316e-05

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.