Coexpression cluster:C684

Full id: C684_pagetoid_mesothelioma_placenta_bone_papillotubular_Hair_Fibroblast

Phase1 CAGE Peaks

Hg19::chr11:12061317..12061323,-	p@chr11:12061317..12061323 -
Hg19::chr12:127762515..127762539,-	p@chr12:127762515..127762539 -
Hg19::chr14:102706939..102706979,-	p4@MOK
Hg19::chr17:49500350..49500395,+	p@chr17:49500350..49500395 +
Hg19::chr19:49547099..49547106,+	p1@CGB5
Hg19::chr22:49818414..49818424,+	p@chr22:49818414..49818424 +
Hg19::chr22:49819110..49819121,-	p5@C22orf34
Hg19::chr2:28201109..28201125,+	p2@BRE
Hg19::chr3:45174403..45174415,+	p@chr3:45174403..45174415 +
Hg19::chr5:174252830..174252847,+	p@chr5:174252830..174252847 +
Hg19::chr5:174252850..174252859,+	p@chr5:174252850..174252859 +
Hg19::chr6:45626924..45626929,+	p@chr6:45626924..45626929 +

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:0000268	peroxisome targeting sequence binding	0.00353232073472271
GO:0045768	positive regulation of anti-apoptosis	0.00706464146944542
GO:0045767	regulation of anti-apoptosis	0.00706464146944542
GO:0005048	signal sequence binding	0.00741787354291769
GO:0000152	nuclear ubiquitin ligase complex	0.00741787354291769
GO:0005164	tumor necrosis factor receptor binding	0.0103446535802594
GO:0032813	tumor necrosis factor receptor superfamily binding	0.0103446535802594
GO:0000151	ubiquitin ligase complex	0.0183239138113741
GO:0006916	anti-apoptosis	0.0333608069390478
GO:0042277	peptide binding	0.0338514070410927
GO:0043066	negative regulation of apoptosis	0.0338514070410927
GO:0043069	negative regulation of programmed cell death	0.0338514070410927
GO:0005125	cytokine activity	0.0421161318370785

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	8.15e-26	180
animal cell	1.65e-17	679
eukaryotic cell	1.65e-17	679
fibroblast	4.99e-17	75
mesodermal cell	3.98e-14	119
muscle precursor cell	2.27e-11	57
myoblast	2.27e-11	57
multi-potent skeletal muscle stem cell	2.27e-11	57
native cell	2.45e-11	722
skin fibroblast	4.92e-11	23
somatic cell	8.64e-11	591
contractile cell	1.13e-10	59
muscle cell	4.84e-10	54
embryonic cell	1.08e-08	248
electrically responsive cell	1.05e-07	60
electrically active cell	1.05e-07	60
smooth muscle cell	1.21e-07	42
smooth muscle myoblast	1.21e-07	42
multi fate stem cell	3.96e-07	430

Uber Anatomy

Ontology term	p-value	n
somite	1.07e-13	83
paraxial mesoderm	1.07e-13	83
presomitic mesoderm	1.07e-13	83
presumptive segmental plate	1.07e-13	83
trunk paraxial mesoderm	1.07e-13	83
presumptive paraxial mesoderm	1.07e-13	83
dermomyotome	4.10e-13	70
trunk mesenchyme	6.04e-13	143
multilaminar epithelium	3.71e-12	82
skeletal muscle tissue	4.59e-10	61
striated muscle tissue	4.59e-10	61
myotome	4.59e-10	61
integument	3.44e-09	45
integumental system	3.44e-09	45
muscle tissue	4.36e-09	63
musculature	4.36e-09	63
musculature of body	4.36e-09	63
skin of body	8.33e-09	40
trunk	2.37e-08	216
organism subdivision	7.98e-08	365
unilaminar epithelium	9.95e-08	138
epithelial tube	4.62e-07	118
mesenchyme	7.05e-07	238
entire embryonic mesenchyme	7.05e-07	238

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)
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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.