Coexpression cluster:C254

Full id: C254_prostate_rhabdomyosarcoma_seminal_Fibroblast_transitionalcell_Smooth_Iris

Phase1 CAGE Peaks

Hg19::chr10:33624520..33624578,-	p@chr10:33624520..33624578 -
Hg19::chr10:38146468..38146475,-	p12@ZNF248
Hg19::chr10:38146482..38146507,-	p4@ZNF248
Hg19::chr10:4808729..4808734,-	p@chr10:4808729..4808734 -
Hg19::chr11:1221057..1221104,+	p1@uc009ycs.1
Hg19::chr11:66583418..66583427,+	p6@C11orf80
Hg19::chr12:52679734..52679755,-	p@chr12:52679734..52679755 -
Hg19::chr13:66882589..66882629,+	p@chr13:66882589..66882629 +
Hg19::chr14:62393999..62394005,+	p@chr14:62393999..62394005 +
Hg19::chr14:62583348..62583354,+	p3@FLJ43390
Hg19::chr15:69339407..69339410,+	p3@NOX5
Hg19::chr15:74220458..74220472,-	p11@LOC100287616
Hg19::chr15:74220487..74220499,-	p9@LOC100287616
Hg19::chr15:74220519..74220531,-	p8@LOC100287616
Hg19::chr15:74220536..74220564,-	p3@LOC100287616
Hg19::chr15:74220590..74220602,-	p15@LOC100287616
Hg19::chr15:74220651..74220670,-	p5@LOC100287616
Hg19::chr17:46806016..46806029,-	p5@HOXB13
Hg19::chr17:46806373..46806386,-	p6@HOXB13
Hg19::chr17:46806404..46806415,-	p7@HOXB13
Hg19::chr17:46806554..46806558,-	p9@HOXB13
Hg19::chr17:49141793..49141801,-	p@chr17:49141793..49141801 -
Hg19::chr1:85395365..85395368,-	p6@MCOLN2
Hg19::chr20:24115408..24115418,+	p@chr20:24115408..24115418 +
Hg19::chr20:58410917..58410928,+	p12@PHACTR3
Hg19::chr20:58411263..58411271,+	p34@PHACTR3
Hg19::chr21:46331846..46331872,-	p29@ITGB2
Hg19::chr22:39410287..39410302,+	p2@APOBEC3C
Hg19::chr2:189992577..189992580,-	p@chr2:189992577..189992580 -
Hg19::chr2:36806022..36806034,-	p20@FEZ2
Hg19::chr3:108160535..108160548,-	p@chr3:108160535..108160548 -
Hg19::chr3:146464294..146464304,+	p@chr3:146464294..146464304 +
Hg19::chr4:69614262..69614265,-	p@chr4:69614262..69614265 -
Hg19::chr5:147297683..147297729,-	p@chr5:147297683..147297729 -
Hg19::chr5:151055872..151055921,-	p14@SPARC
Hg19::chr6:47010258..47010273,-	p5@GPR110
Hg19::chr6:47010286..47010292,-	p11@GPR110
Hg19::chr6:47010305..47010311,-	p8@GPR110
Hg19::chr7:103086717..103086724,+	p@chr7:103086717..103086724 +
Hg19::chr7:103086740..103086747,+	p@chr7:103086740..103086747 +
Hg19::chr7:103310094..103310097,+	p@chr7:103310094..103310097 +
Hg19::chr7:31855776..31855807,-	p@chr7:31855776..31855807 -
Hg19::chr7:48251843..48251884,+	p@chr7:48251843..48251884 +
Hg19::chr8:38687332..38687338,+	p@chr8:38687332..38687338 +
Hg19::chr9:123788118..123788127,-	p@chr9:123788118..123788127 -
Hg19::chr9:35753022..35753030,-	p4@CU674847
Hg19::chr9:35753038..35753047,-	p2@CU674847
Hg19::chr9:35753063..35753064,-	p5@CU674847
Hg19::chr9:35754222..35754237,-	p3@MSMP
Hg19::chr9:35754253..35754279,-	p1@MSMP
Hg19::chr9:35754350..35754382,-	p4@MSMP

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:0043012	regulation of fusion of sperm to egg plasma membrane	0.0376730967742162
GO:0010155	regulation of proton transport	0.0376730967742162
GO:0015252	hydrogen ion channel activity	0.0376730967742162
GO:0016175	superoxide-generating NADPH oxidase activity	0.0376730967742162

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	1.31e-20	180
mesodermal cell	2.12e-18	119
embryonic cell	9.42e-15	248
contractile cell	1.06e-12	59
muscle precursor cell	8.58e-12	57
myoblast	8.58e-12	57
multi-potent skeletal muscle stem cell	8.58e-12	57
animal cell	1.17e-11	679
eukaryotic cell	1.17e-11	679
muscle cell	5.83e-11	54
somatic cell	1.21e-10	591
fibroblast	1.48e-09	75
smooth muscle cell	8.68e-09	42
smooth muscle myoblast	8.68e-09	42
electrically responsive cell	1.20e-08	60
electrically active cell	1.20e-08	60
native cell	5.58e-08	722
vascular associated smooth muscle cell	1.86e-07	32
lining cell	2.82e-07	57
barrier cell	2.82e-07	57
endothelial cell of vascular tree	5.34e-07	24

Uber Anatomy

Ontology term	p-value	n
vasculature	5.94e-16	79
vascular system	5.94e-16	79
cardiovascular system	2.45e-12	110
vessel	3.30e-12	69
trunk mesenchyme	3.40e-12	143
somite	4.86e-12	83
paraxial mesoderm	4.86e-12	83
presomitic mesoderm	4.86e-12	83
presumptive segmental plate	4.86e-12	83
trunk paraxial mesoderm	4.86e-12	83
presumptive paraxial mesoderm	4.86e-12	83
trunk	6.16e-12	216
unilaminar epithelium	7.40e-12	138
multilaminar epithelium	9.31e-12	82
circulatory system	1.92e-11	113
dermomyotome	1.14e-10	70
blood vessel	1.89e-10	60
epithelial tube open at both ends	1.89e-10	60
blood vasculature	1.89e-10	60
vascular cord	1.89e-10	60
artery	6.23e-10	42
arterial blood vessel	6.23e-10	42
arterial system	6.23e-10	42
epithelial tube	1.95e-09	118
mesenchyme	2.05e-09	238
entire embryonic mesenchyme	2.05e-09	238
skeletal muscle tissue	3.95e-09	61
striated muscle tissue	3.95e-09	61
myotome	3.95e-09	61
systemic artery	4.56e-09	33
systemic arterial system	4.56e-09	33
splanchnic layer of lateral plate mesoderm	8.59e-09	84
muscle tissue	2.37e-08	63
musculature	2.37e-08	63
musculature of body	2.37e-08	63
organism subdivision	4.45e-07	365
cell layer	6.19e-07	312

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
ZZZ3#26009	3	14.083130143249	0.00130203389673015	0.0087224578666196

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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