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><br>

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Cell Type

Ontology term	p-value	n
non-terminally differentiated cell	5.25e-31	180
fibroblast	6.99e-18	75
muscle precursor cell	2.43e-16	57
myoblast	2.43e-16	57
multi-potent skeletal muscle stem cell	2.43e-16	57
muscle cell	4.37e-16	54
contractile cell	6.97e-16	59
electrically responsive cell	1.11e-13	60
electrically active cell	1.11e-13	60
smooth muscle cell	3.90e-12	42
smooth muscle myoblast	3.90e-12	42
vascular associated smooth muscle cell	1.48e-08	32
mesodermal cell	3.17e-07	119
fat cell	3.64e-07	15
cardiocyte	7.21e-07	16

Uber Anatomy

Ontology term	p-value	n
somite	2.65e-19	83
paraxial mesoderm	2.65e-19	83
presomitic mesoderm	2.65e-19	83
presumptive segmental plate	2.65e-19	83
trunk paraxial mesoderm	2.65e-19	83
presumptive paraxial mesoderm	2.65e-19	83
dermomyotome	3.51e-18	70
muscle tissue	1.45e-17	63
musculature	1.45e-17	63
musculature of body	1.45e-17	63
skeletal muscle tissue	2.16e-17	61
striated muscle tissue	2.16e-17	61
myotome	2.16e-17	61
trunk mesenchyme	6.66e-16	143
multilaminar epithelium	1.59e-13	82
multi-tissue structure	1.98e-12	347
multi-cellular organism	1.44e-11	659
organism subdivision	4.13e-11	365
trunk	4.40e-11	216
mesenchyme	4.57e-11	238
entire embryonic mesenchyme	4.57e-11	238
splanchnic layer of lateral plate mesoderm	4.24e-10	84
primary circulatory organ	3.86e-08	27
heart	3.96e-08	24
primitive heart tube	3.96e-08	24
primary heart field	3.96e-08	24
anterior lateral plate mesoderm	3.96e-08	24
heart tube	3.96e-08	24
heart primordium	3.96e-08	24
cardiac mesoderm	3.96e-08	24
cardiogenic plate	3.96e-08	24
heart rudiment	3.96e-08	24
unilaminar epithelium	1.71e-07	138
adipose tissue	3.44e-07	14
extraembryonic structure	4.12e-07	24
organ component layer	4.96e-07	57
tissue	7.91e-07	787
mesoderm	8.49e-07	448
mesoderm-derived structure	8.49e-07	448
presumptive mesoderm	8.49e-07	448

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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