Coexpression cluster:C463

Full id: C463_Mesothelial_mesothelioma_Sertoli_mesenchymal_vagina_Cardiac_Fibroblast

Phase1 CAGE Peaks

Hg19::chr10:6622278..6622290,-	p6@PRKCQ
Hg19::chr11:116728907..116728948,+	p2@CU690121
Hg19::chr13:38091764..38091775,+	p@chr13:38091764..38091775 +
Hg19::chr13:38145825..38145840,-	p14@POSTN
Hg19::chr13:38148733..38148753,-	p@chr13:38148733..38148753 -
Hg19::chr13:97328912..97328917,+	p@chr13:97328912..97328917 +
Hg19::chr1:22469560..22469567,-	p3@WNT4
Hg19::chr20:6033732..6033760,-	p8@AB527789
Hg19::chr20:6034216..6034224,-	p@chr20:6034216..6034224 -
Hg19::chr20:6034506..6034518,-	p4@LRRN4
Hg19::chr20:61687988..61688007,-	p@chr20:61687988..61688007 -
Hg19::chr20:8101412..8101426,+	p@chr20:8101412..8101426 +
Hg19::chr20:8101451..8101452,+	p@chr20:8101451..8101452 +
Hg19::chr2:10454550..10454555,+	p@chr2:10454550..10454555 +
Hg19::chr2:220309299..220309306,+	p32@SPEG
Hg19::chr3:158450428..158450431,-	p9@RARRES1
Hg19::chr3:158450447..158450473,-	p4@RARRES1
Hg19::chr3:158450475..158450494,-	p6@RARRES1
Hg19::chr3:180707620..180707631,-	p3@DNAJC19
Hg19::chr4:146267392..146267393,-	p@chr4:146267392..146267393 -
Hg19::chr8:140663726..140663732,-	p@chr8:140663726..140663732 -

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:0032502	developmental process	0.00688389882661927
GO:0048856	anatomical structure development	0.0111239349841107
GO:0007275	multicellular organismal development	0.0126389772157664
GO:0008285	negative regulation of cell proliferation	0.0189097449991574
GO:0048513	organ development	0.0189097449991574
GO:0048731	system development	0.0285564188245063
GO:0032501	multicellular organismal process	0.0285564188245063
GO:0048806	genitalia development	0.0285564188245063
GO:0005578	proteinaceous extracellular matrix	0.0285564188245063
GO:0043681	protein import into mitochondrion	0.0285564188245063
GO:0004697	protein kinase C activity	0.0285564188245063
GO:0001565	phorbol ester receptor activity	0.0285564188245063
GO:0042127	regulation of cell proliferation	0.0285564188245063

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
contractile cell	4.18e-10	59
muscle cell	1.18e-09	54
muscle precursor cell	1.11e-08	57
myoblast	1.11e-08	57
multi-potent skeletal muscle stem cell	1.11e-08	57
electrically responsive cell	1.71e-08	60
electrically active cell	1.71e-08	60
smooth muscle cell	5.56e-08	42
smooth muscle myoblast	5.56e-08	42
mesodermal cell	1.37e-07	119
vascular associated smooth muscle cell	4.65e-07	32

Uber Anatomy

Ontology term	p-value	n
epithelial tube	6.06e-12	118
trunk mesenchyme	6.66e-11	143
multi-tissue structure	1.99e-09	347
muscle tissue	5.38e-09	63
musculature	5.38e-09	63
musculature of body	5.38e-09	63
compound organ	7.53e-09	69
trunk	1.04e-08	216
anatomical cluster	1.33e-08	286
cell layer	1.62e-08	312
skeletal muscle tissue	2.54e-08	61
striated muscle tissue	2.54e-08	61
myotome	2.54e-08	61
epithelium	4.25e-08	309
anatomical conduit	5.46e-08	241
unilaminar epithelium	8.09e-08	138
primary circulatory organ	1.21e-07	27
tube	1.63e-07	194
mesenchyme	2.37e-07	238
entire embryonic mesenchyme	2.37e-07	238
splanchnic layer of lateral plate mesoderm	3.34e-07	84
heart	5.28e-07	24
primitive heart tube	5.28e-07	24
primary heart field	5.28e-07	24
anterior lateral plate mesoderm	5.28e-07	24
heart tube	5.28e-07	24
heart primordium	5.28e-07	24
cardiac mesoderm	5.28e-07	24
cardiogenic plate	5.28e-07	24
heart rudiment	5.28e-07	24
systemic artery	6.90e-07	33
systemic arterial system	6.90e-07	33

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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This analysis result is provided for C0 - C305 clusters.