Coexpression cluster:C292

Full id: C292_Mesenchymal_skin_umbilical_Adipocyte_mesenchymal_Chondrocyte_skeletal

Phase1 CAGE Peaks

Hg19::chr17:48261721..48261729,-	p@chr17:48261721..48261729 -
Hg19::chr2:189839090..189839105,+	p1@COL3A1
Hg19::chr2:189849579..189849628,+	p@chr2:189849579..189849628 +
Hg19::chr2:189849915..189849949,+	p@chr2:189849915..189849949 +
Hg19::chr2:189850401..189850478,+	p@chr2:189850401..189850478 +
Hg19::chr2:189851773..189851845,+	p4@COL3A1
Hg19::chr2:189852804..189852835,+	p@chr2:189852804..189852835 +
Hg19::chr2:189855724..189855761,+	p@chr2:189855724..189855761 +
Hg19::chr2:189856903..189856926,+	p@chr2:189856903..189856926 +
Hg19::chr2:189857607..189857646,+	p@chr2:189857607..189857646 +
Hg19::chr2:189858077..189858096,+	p@chr2:189858077..189858096 +
Hg19::chr2:189858136..189858149,+	p@chr2:189858136..189858149 +
Hg19::chr2:189858758..189858780,+	p@chr2:189858758..189858780 +
Hg19::chr2:189858991..189859033,+	p@chr2:189858991..189859033 +
Hg19::chr2:189859261..189859297,+	p@chr2:189859261..189859297 +
Hg19::chr2:189859443..189859507,+	p@chr2:189859443..189859507 +
Hg19::chr2:189861175..189861198,+	p@chr2:189861175..189861198 +
Hg19::chr2:189864003..189864023,+	p@chr2:189864003..189864023 +
Hg19::chr2:189864188..189864235,+	p@chr2:189864188..189864235 +
Hg19::chr2:189864267..189864279,+	p@chr2:189864267..189864279 +
Hg19::chr2:189866256..189866277,+	p@chr2:189866256..189866277 +
Hg19::chr2:189867024..189867049,+	p@chr2:189867024..189867049 +
Hg19::chr2:189869053..189869071,+	p19@COL3A1
Hg19::chr2:189873664..189873737,+	p2@COL3A1
Hg19::chr2:189873740..189873791,+	p3@COL3A1
Hg19::chr2:189873796..189873815,+	p12@COL3A1
Hg19::chr2:189873877..189873903,+	p10@COL3A1
Hg19::chr2:189874898..189874924,+	p@chr2:189874898..189874924 +
Hg19::chr2:189874955..189875006,+	p@chr2:189874955..189875006 +
Hg19::chr2:189875363..189875390,+	p@chr2:189875363..189875390 +
Hg19::chr2:189875404..189875442,+	p@chr2:189875404..189875442 +
Hg19::chr2:189875563..189875584,+	p@chr2:189875563..189875584 +
Hg19::chr2:189876360..189876377,+	p4@AF130082
Hg19::chr2:189876383..189876417,+	p3@AF130082
Hg19::chr2:189876466..189876506,+	p1@AF130082
Hg19::chr2:189876532..189876594,+	p2@AF130082
Hg19::chr2:189876664..189876675,+	p10@AF130082
Hg19::chr2:189876710..189876721,+	p7@AF130082
Hg19::chr2:189876741..189876752,+	p9@AF130082
Hg19::chr2:189876820..189876830,+	p11@AF130082
Hg19::chr2:189876888..189876899,+	p12@AF130082
Hg19::chr2:189877182..189877191,+	p@chr2:189877182..189877191 +
Hg19::chr2:189877298..189877309,+	p@chr2:189877298..189877309 +
Hg19::chr2:189877348..189877367,+	p@chr2:189877348..189877367 +

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:0005586	collagen type III	0.000853644177557989
GO:0005583	fibrillar collagen	0.00469504297656894
GO:0005581	collagen	0.0153655951960438
GO:0005201	extracellular matrix structural constituent	0.0170728835511598
GO:0044420	extracellular matrix part	0.0170728835511598
GO:0006817	phosphate transport	0.0170728835511598
GO:0003013	circulatory system process	0.0170728835511598
GO:0008015	blood circulation	0.0170728835511598
GO:0015698	inorganic anion transport	0.0246608317961197
GO:0006820	anion transport	0.027572706935123
GO:0009887	organ morphogenesis	0.028092653843272
GO:0005578	proteinaceous extracellular matrix	0.0299486832293261

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
fibroblast	1.10e-20	76
muscle cell	1.76e-15	55
contractile cell	2.02e-15	59
muscle precursor cell	2.18e-15	58
myoblast	2.18e-15	58
multi-potent skeletal muscle stem cell	2.18e-15	58
electrically responsive cell	1.72e-12	61
electrically active cell	1.72e-12	61
multi fate stem cell	2.56e-12	427
somatic stem cell	1.73e-11	433
stem cell	5.54e-11	441
smooth muscle cell	7.13e-11	43
smooth muscle myoblast	7.13e-11	43
extraembryonic cell	4.04e-10	19
non-terminally differentiated cell	1.45e-09	106
preadipocyte	4.11e-08	12
cardiocyte	4.43e-08	16
stromal cell	2.39e-07	28
extracellular matrix secreting cell	6.63e-07	15

Uber Anatomy

Ontology term	p-value	n
muscle tissue	3.39e-16	64
musculature	3.39e-16	64
musculature of body	3.39e-16	64
skeletal muscle tissue	8.20e-16	62
striated muscle tissue	8.20e-16	62
myotome	8.20e-16	62
dense mesenchyme tissue	3.33e-15	73
somite	4.04e-15	71
presomitic mesoderm	4.04e-15	71
presumptive segmental plate	4.04e-15	71
dermomyotome	4.04e-15	71
trunk paraxial mesoderm	4.04e-15	71
paraxial mesoderm	1.14e-14	72
presumptive paraxial mesoderm	1.14e-14	72
mesenchyme	1.51e-12	160
entire embryonic mesenchyme	1.51e-12	160
epithelial vesicle	3.07e-12	78
multilaminar epithelium	5.24e-12	83
trunk mesenchyme	6.52e-11	122
mesoderm	1.48e-10	315
mesoderm-derived structure	1.48e-10	315
presumptive mesoderm	1.48e-10	315
extraembryonic structure	4.94e-09	24
splanchnic layer of lateral plate mesoderm	1.83e-08	83
heart	4.16e-08	24
primitive heart tube	4.16e-08	24
primary heart field	4.16e-08	24
anterior lateral plate mesoderm	4.16e-08	24
heart tube	4.16e-08	24
heart primordium	4.16e-08	24
cardiac mesoderm	4.16e-08	24
cardiogenic plate	4.16e-08	24
heart rudiment	4.16e-08	24
adipose tissue	2.56e-07	14
primary circulatory organ	3.08e-07	27
trunk	4.32e-07	199
organ component layer	5.21e-07	66

Disease

Ontology term	p-value	n
ovarian cancer	3.53e-08	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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