Coexpression cluster:C243

Full id: C243_Chondrocyte_trachea_Synoviocyte_mesodermal_renal_Fibroblast_Ewing

Phase1 CAGE Peaks

Hg19::chr10:73730296..73730317,+	p@chr10:73730296..73730317 +
Hg19::chr10:99790340..99790353,-	p2@CRTAC1
Hg19::chr10:99790370..99790385,-	p1@CRTAC1
Hg19::chr12:48367311..48367320,-	p14@HNRNPM
Hg19::chr12:48398250..48398267,-	p1@COL2A1
Hg19::chr12:53447073..53447087,+	p@chr12:53447073..53447087 +
Hg19::chr12:57628783..57628814,+	p@chr12:57628783..57628814 +
Hg19::chr12:57629169..57629214,-	p@chr12:57629169..57629214 -
Hg19::chr12:57629234..57629249,-	p@chr12:57629234..57629249 -
Hg19::chr12:57629315..57629334,-	p@chr12:57629315..57629334 -
Hg19::chr12:57629562..57629589,-	p@chr12:57629562..57629589 -
Hg19::chr12:57630410..57630437,-	p@chr12:57630410..57630437 -
Hg19::chr12:57630458..57630470,-	p@chr12:57630458..57630470 -
Hg19::chr12:57630873..57630895,-	p1@NDUFA4L2
Hg19::chr12:57630900..57630911,-	p2@NDUFA4L2
Hg19::chr15:89346657..89346673,+	p1@ACAN
Hg19::chr15:89346682..89346691,+	p4@ACAN
Hg19::chr15:89346699..89346715,+	p2@ACAN
Hg19::chr15:89346739..89346750,+	p3@ACAN
Hg19::chr15:89381951..89381962,+	p@chr15:89381951..89381962 +
Hg19::chr15:89401833..89401842,+	p10@ACAN
Hg19::chr15:89402048..89402061,+	p8@ACAN
Hg19::chr15:89402148..89402159,+	p6@ACAN
Hg19::chr15:89417758..89417770,+	p@chr15:89417758..89417770 +
Hg19::chr16:69958887..69958927,+	p3@WWP2
Hg19::chr16:69958930..69958953,+	p2@WWP2
Hg19::chr16:69958959..69958971,+	p6@WWP2
Hg19::chr17:26127550..26127556,-	p1@NOS2
Hg19::chr19:41281416..41281445,+	p1@MIA-RAB4B
Hg19::chr1:111770265..111770275,+	p10@CHI3L2
Hg19::chr1:111770278..111770289,+	p9@CHI3L2
Hg19::chr1:111770294..111770305,+	p6@CHI3L2
Hg19::chr1:111770322..111770342,+	p1@CHI3L2
Hg19::chr1:111773349..111773368,+	p11@CHI3L2
Hg19::chr1:186273999..186274008,+	p@chr1:186273999..186274008 +
Hg19::chr1:186276610..186276616,+	p@chr1:186276610..186276616 +
Hg19::chr1:186277391..186277396,+	p@chr1:186277391..186277396 +
Hg19::chr1:203316798..203316810,-	p13@FMOD
Hg19::chr1:2066360..2066369,+	p36@PRKCZ
Hg19::chr20:43936937..43936967,-	p1@MATN4
Hg19::chr21:40033882..40033887,-	p21@ERG
Hg19::chr2:216252918..216252935,-	p@chr2:216252918..216252935 -
Hg19::chr2:216300502..216300517,+	p4@ENST00000412951
Hg19::chr2:233734789..233734820,+	p4@C2orf82
Hg19::chr2:233735030..233735044,+	p3@C2orf82
Hg19::chr3:140981491..140981508,+	p3@ACPL2
Hg19::chr3:142607876..142607887,-	p7@PCOLCE2
Hg19::chr4:174320254..174320274,-	p2@SCRG1
Hg19::chr4:174320281..174320304,-	p3@SCRG1
Hg19::chr6:33160233..33160251,-	p1@COL11A2
Hg19::chr8:57354045..57354055,-	p@chr8:57354045..57354055 -
Hg19::chr9:130636920..130636950,-	p5@AK1
Hg19::chr9:131168253..131168264,+	p@chr9:131168253..131168264 +
Hg19::chr9:131168289..131168300,+	p@chr9:131168289..131168300 +
Hg19::chrX:54824686..54824690,-	p1@ITIH6

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
3.89935446244208e-05	0.0246829137472584	3	106	Amoebiasis (KEGG):05146
0.000120675008846136	0.0381936402998021	3	155	IL-1 up reg. targets (Netpath):NetPath_13

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:0044421	extracellular region part	0.000205191071528448
GO:0005583	fibrillar collagen	0.000978053245048239
GO:0005201	extracellular matrix structural constituent	0.00119181646855413
GO:0005578	proteinaceous extracellular matrix	0.00119181646855413
GO:0001501	skeletal development	0.00359209545847259
GO:0030198	extracellular matrix organization and biogenesis	0.00608470421680022
GO:0005581	collagen	0.00719737186271699
GO:0005585	collagen type II	0.0116419404215236
GO:0043062	extracellular structure organization and biogenesis	0.0135409792303694
GO:0005592	collagen type XI	0.0153553945672956
GO:0030020	extracellular matrix structural constituent conferring tensile strength	0.0153553945672956
GO:0005539	glycosaminoglycan binding	0.0153553945672956
GO:0030247	polysaccharide binding	0.0153553945672956
GO:0001871	pattern binding	0.0153553945672956
GO:0005584	collagen type I	0.0153553945672956
GO:0004700	atypical protein kinase C activity	0.0153553945672956
GO:0044420	extracellular matrix part	0.0153553945672956
GO:0050954	sensory perception of mechanical stimulus	0.0153553945672956
GO:0007605	sensory perception of sound	0.0153553945672956
GO:0032502	developmental process	0.0153553945672956
GO:0006817	phosphate transport	0.0165717751341296
GO:0007181	transforming growth factor beta receptor complex assembly	0.0165717751341296
GO:0007275	multicellular organismal development	0.0165717751341296
GO:0030021	extracellular matrix structural constituent conferring compression resistance	0.0271333600942556
GO:0048731	system development	0.0300744875262851
GO:0030199	collagen fibril organization	0.0300744875262851
GO:0044409	entry into host	0.0300744875262851
GO:0030260	entry into host cell	0.0300744875262851
GO:0019059	initiation of viral infection	0.0300744875262851
GO:0052192	movement in environment of other organism during symbiotic interaction	0.0300744875262851
GO:0046718	entry of virus into host cell	0.0300744875262851
GO:0052126	movement in host environment	0.0300744875262851
GO:0051828	entry into other organism during symbiotic interaction	0.0300744875262851
GO:0051806	entry into cell of other organism during symbiotic interaction	0.0300744875262851
GO:0015698	inorganic anion transport	0.0316658241886977
GO:0004017	adenylate kinase activity	0.0316658241886977
GO:0006032	chitin catabolic process	0.0316658241886977
GO:0006046	N-acetylglucosamine catabolic process	0.0316658241886977
GO:0006043	glucosamine catabolic process	0.0316658241886977
GO:0046348	amino sugar catabolic process	0.0316658241886977
GO:0004697	protein kinase C activity	0.0316658241886977
GO:0006030	chitin metabolic process	0.0316658241886977
GO:0004568	chitinase activity	0.0316658241886977
GO:0001565	phorbol ester receptor activity	0.0316658241886977
GO:0048856	anatomical structure development	0.0373617123603633
GO:0006820	anion transport	0.0373617123603633
GO:0044247	cellular polysaccharide catabolic process	0.0405912102693347
GO:0000272	polysaccharide catabolic process	0.0405912102693347
GO:0051701	interaction with host	0.0416483223058567
GO:0048513	organ development	0.0471112555794051

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
GAG secreting cell	1.20e-19	9
carbohydrate secreting cell	1.20e-19	9
collagen secreting cell	1.21e-15	6
chondroblast	1.21e-15	6
chondrocyte	1.21e-15	6
extracellular matrix secreting cell	2.58e-11	15
stromal cell	3.62e-07	28

Uber Anatomy

Ontology term	p-value	n
adult organism	1.37e-38	114
neural tube	1.13e-17	56
neural rod	1.13e-17	56
future spinal cord	1.13e-17	56
neural keel	1.13e-17	56
central nervous system	6.42e-15	81
regional part of nervous system	8.54e-15	53
regional part of brain	8.54e-15	53
neural plate	2.32e-13	82
presumptive neural plate	2.32e-13	82
nervous system	6.55e-13	89
brain grey matter	1.46e-12	34
gray matter	1.46e-12	34
neurectoderm	1.67e-12	86
telencephalon	1.85e-12	34
brain	7.78e-12	68
future brain	7.78e-12	68
regional part of forebrain	1.14e-11	41
forebrain	1.14e-11	41
anterior neural tube	1.14e-11	41
future forebrain	1.14e-11	41
regional part of telencephalon	2.42e-11	32
structure with developmental contribution from neural crest	4.96e-11	132
ecto-epithelium	1.22e-10	104
neocortex	1.24e-10	20
regional part of cerebral cortex	1.43e-09	22
cerebral hemisphere	2.18e-09	32
organ system subdivision	4.00e-09	223
brainstem	5.42e-09	6
open tracheal system trachea	1.82e-08	2
cerebral cortex	2.76e-08	25
pallium	2.76e-08	25
throat	3.09e-08	2
meninx	4.09e-08	2
membrane organ	4.09e-08	2
meningeal cluster	4.09e-08	2
pre-chordal neural plate	4.26e-08	61
ectoderm-derived structure	8.02e-08	171
ectoderm	8.02e-08	171
presumptive ectoderm	8.02e-08	171
posterior neural tube	1.59e-07	15
chordal neural plate	1.59e-07	15

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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