Coexpression cluster:C830

Full id: C830_Renal_Endothelial_adipose_Mast_ovary_testis_Lymphatic

Phase1 CAGE Peaks

Hg19::chr14:54421190..54421212,-	p5@BMP4
Hg19::chr19:50192842..50192863,+	p2@C19orf76
Hg19::chr2:20647026..20647047,+	p5@RHOB
Hg19::chr2:20647862..20647881,+	p4@RHOB
Hg19::chr2:26700331..26700340,-	p@chr2:26700331..26700340 -
Hg19::chr2:26700872..26700884,-	p5@OTOF
Hg19::chr2:26700900..26700918,-	p4@OTOF
Hg19::chr2:26700923..26700934,-	p9@OTOF
Hg19::chr2:26700984..26700993,-	p7@OTOF
Hg19::chr5:150019594..150019618,+	p@chr5:150019594..150019618 +

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:0001525	angiogenesis	0.00352018488905965
GO:0048514	blood vessel morphogenesis	0.00352018488905965
GO:0048646	anatomical structure formation	0.00352018488905965
GO:0001568	blood vessel development	0.00352018488905965
GO:0001944	vasculature development	0.00352018488905965
GO:0021904	dorsoventral neural tube patterning	0.00365006475921347
GO:0045786	negative regulation of progression through cell cycle	0.0043799487752665
GO:0032331	negative regulation of chondrocyte differentiation	0.0043799487752665
GO:0021532	neural tube patterning	0.0043799487752665
GO:0021978	telencephalon regionalization	0.0043799487752665
GO:0006927	transformed cell apoptosis	0.00461020095924032
GO:0045662	negative regulation of myoblast differentiation	0.00461020095924032
GO:0030501	positive regulation of bone mineralization	0.00461020095924032
GO:0000074	regulation of progression through cell cycle	0.00461020095924032
GO:0051726	regulation of cell cycle	0.00461020095924032
GO:0009887	organ morphogenesis	0.00461020095924032
GO:0032330	regulation of chondrocyte differentiation	0.00461020095924032
GO:0007500	mesodermal cell fate determination	0.00461020095924032
GO:0021871	forebrain regionalization	0.00461020095924032
GO:0045669	positive regulation of osteoblast differentiation	0.00547445247884972
GO:0008333	endosome to lysosome transport	0.00571230398792825
GO:0045778	positive regulation of ossification	0.00571230398792825
GO:0045661	regulation of myoblast differentiation	0.00571230398792825
GO:0046852	positive regulation of bone remodeling	0.00589521710383024
GO:0001710	mesodermal cell fate commitment	0.00589521710383024
GO:0048333	mesodermal cell differentiation	0.00589521710383024
GO:0051145	smooth muscle cell differentiation	0.00625596459095219
GO:0045843	negative regulation of striated muscle development	0.00625596459095219
GO:0002062	chondrocyte differentiation	0.00679507183798379
GO:0045667	regulation of osteoblast differentiation	0.00706276996781126
GO:0001658	ureteric bud branching	0.00706276996781126
GO:0030500	regulation of bone mineralization	0.00752578033711717
GO:0022402	cell cycle process	0.00752578033711717
GO:0045766	positive regulation of angiogenesis	0.00772704627624871
GO:0016202	regulation of striated muscle development	0.00813155691880163
GO:0007041	lysosomal transport	0.00851355894503422
GO:0001707	mesoderm formation	0.00887487737891711
GO:0032501	multicellular organismal process	0.00904102041585094
GO:0048332	mesoderm morphogenesis	0.00904102041585094
GO:0001704	formation of primary germ layer	0.00904102041585094
GO:0030509	BMP signaling pathway	0.00904102041585094
GO:0001657	ureteric bud development	0.00904102041585094
GO:0042475	odontogenesis of dentine-containing teeth	0.00904102041585094
GO:0021915	neural tube development	0.00904102041585094
GO:0030278	regulation of ossification	0.00904102041585094
GO:0007281	germ cell development	0.00904102041585094
GO:0030282	bone mineralization	0.00928784922746442
GO:0007049	cell cycle	0.00928784922746442
GO:0046850	regulation of bone remodeling	0.0101319072928017
GO:0001656	metanephros development	0.0101319072928017
GO:0042476	odontogenesis	0.0101319072928017
GO:0001649	osteoblast differentiation	0.0101319072928017
GO:0007034	vacuolar transport	0.0101319072928017
GO:0007369	gastrulation	0.0101319072928017
GO:0045445	myoblast differentiation	0.0101872075412325
GO:0001934	positive regulation of protein amino acid phosphorylation	0.0101872075412325
GO:0033240	positive regulation of amine metabolic process	0.0101872075412325
GO:0045764	positive regulation of amino acid metabolic process	0.0101872075412325
GO:0048754	branching morphogenesis of a tube	0.0102120604434338
GO:0009953	dorsal/ventral pattern formation	0.0102120604434338
GO:0031902	late endosome membrane	0.010235289153024
GO:0001709	cell fate determination	0.010235289153024
GO:0009653	anatomical structure morphogenesis	0.0109402046955137
GO:0001763	morphogenesis of a branching structure	0.0109402046955137
GO:0030218	erythrocyte differentiation	0.0111081884375619
GO:0043010	camera-type eye development	0.0112710622458616
GO:0051216	cartilage development	0.0115459537040865
GO:0001822	kidney development	0.0115459537040865
GO:0006944	membrane fusion	0.0115459537040865
GO:0048523	negative regulation of cellular process	0.0115459537040865
GO:0048513	organ development	0.0115459537040865
GO:0045765	regulation of angiogenesis	0.0115459537040865
GO:0001655	urogenital system development	0.0116809668371001
GO:0016197	endosome transport	0.0116809668371001
GO:0048519	negative regulation of biological process	0.0116809668371001
GO:0048741	skeletal muscle fiber development	0.0116809668371001
GO:0030324	lung development	0.0116809668371001
GO:0048747	muscle fiber development	0.0116809668371001
GO:0030323	respiratory tube development	0.0116809668371001
GO:0007498	mesoderm development	0.0116809668371001
GO:0048468	cell development	0.0116809668371001
GO:0001932	regulation of protein amino acid phosphorylation	0.0116809668371001
GO:0030900	forebrain development	0.0116809668371001
GO:0033238	regulation of amine metabolic process	0.0116809668371001
GO:0042692	muscle cell differentiation	0.0116809668371001
GO:0006521	regulation of amino acid metabolic process	0.0116809668371001
GO:0045597	positive regulation of cell differentiation	0.0116809668371001
GO:0001654	eye development	0.0116809668371001
GO:0005770	late endosome	0.0125311986003383
GO:0042325	regulation of phosphorylation	0.01554474559342
GO:0045596	negative regulation of cell differentiation	0.0156136818634785
GO:0007519	skeletal muscle development	0.0158747785825665
GO:0051094	positive regulation of developmental process	0.0158747785825665
GO:0051174	regulation of phosphorus metabolic process	0.0158747785825665
GO:0019220	regulation of phosphate metabolic process	0.0158747785825665
GO:0045165	cell fate commitment	0.0161638094001479
GO:0048729	tissue morphogenesis	0.0162220066069993
GO:0048731	system development	0.0164026782168303
GO:0008201	heparin binding	0.0164956866080014
GO:0007178	transmembrane receptor protein serine/threonine kinase signaling pathway	0.0164956866080014
GO:0030099	myeloid cell differentiation	0.0164956866080014
GO:0051093	negative regulation of developmental process	0.0164956866080014
GO:0035239	tube morphogenesis	0.0174754790541053
GO:0007423	sensory organ development	0.0174754790541053
GO:0044440	endosomal part	0.0174754790541053
GO:0010008	endosome membrane	0.0174754790541053
GO:0003002	regionalization	0.0174754790541053
GO:0014706	striated muscle development	0.0174754790541053
GO:0001503	ossification	0.0174754790541053
GO:0031214	biomineral formation	0.0174754790541053
GO:0048869	cellular developmental process	0.0180416102903668
GO:0030154	cell differentiation	0.0180416102903668
GO:0007507	heart development	0.0180416102903668
GO:0009792	embryonic development ending in birth or egg hatching	0.0180416102903668
GO:0043009	chordate embryonic development	0.0180416102903668
GO:0046849	bone remodeling	0.0180738211415503
GO:0051240	positive regulation of multicellular organismal process	0.0194280340625341
GO:0048771	tissue remodeling	0.0194280340625341
GO:0005539	glycosaminoglycan binding	0.0201791700177027
GO:0048856	anatomical structure development	0.020737575069496
GO:0030247	polysaccharide binding	0.0209244188058977
GO:0035295	tube development	0.0209311946862125
GO:0007389	pattern specification process	0.0219985960043331
GO:0001871	pattern binding	0.0223471439314306
GO:0050954	sensory perception of mechanical stimulus	0.0228549025510702
GO:0007605	sensory perception of sound	0.0228549025510702
GO:0007420	brain development	0.0238724756048115
GO:0045595	regulation of cell differentiation	0.0245343689107644
GO:0007275	multicellular organismal development	0.0252121697359094
GO:0030097	hemopoiesis	0.0269952425986517
GO:0007517	muscle development	0.0285576995570027
GO:0048534	hemopoietic or lymphoid organ development	0.0285576995570027
GO:0002520	immune system development	0.0298095579949197
GO:0007266	Rho protein signal transduction	0.0305570901556772
GO:0005768	endosome	0.0311328188244837
GO:0001501	skeletal development	0.0334500930167917
GO:0007417	central nervous system development	0.0369267618751606
GO:0009790	embryonic development	0.0369267618751606
GO:0050793	regulation of developmental process	0.0369267618751606
GO:0008083	growth factor activity	0.0392842670450358
GO:0007276	gamete generation	0.0406883426001273
GO:0003924	GTPase activity	0.0419198021015244
GO:0051239	regulation of multicellular organismal process	0.0420786967399136
GO:0016044	membrane organization and biogenesis	0.0428336082681813
GO:0016043	cellular component organization and biogenesis	0.0446058764501163
GO:0007167	enzyme linked receptor protein signaling pathway	0.0446058764501163
GO:0009888	tissue development	0.0450341605435387
GO:0005125	cytokine activity	0.0452741436959324
GO:0032502	developmental process	0.0452741436959324
GO:0019953	sexual reproduction	0.045567020297071

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
endothelial cell	3.82e-14	36
lymphangioblast	7.18e-14	6
endothelial cell of lymphatic vessel	7.18e-14	6
vascular lymphangioblast	7.18e-14	6
endothelial cell of vascular tree	7.86e-14	24
meso-epithelial cell	1.28e-10	45
lining cell	1.68e-07	58
barrier cell	1.68e-07	58

Uber Anatomy

Ontology term	p-value	n
adult organism	1.51e-23	114
lymphatic vessel	2.75e-10	8
lymph vasculature	2.75e-10	8
lymphatic part of lymphoid system	2.75e-10	8
anatomical cluster	2.25e-08	373
anatomical conduit	2.36e-08	240
lymphoid system	3.91e-08	10
brainstem	6.84e-08	6
throat	2.53e-07	2

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
NR3C1#2908	4	5.98920933246922	0.00301039080914885	0.015987907740488
TFAP2A#7020	5	8.25931718652248	0.000158182952393598	0.00199402164937054
TFAP2C#7022	5	5.40461430493011	0.00114527086823733	0.007834093804548

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.