Coexpression cluster:C556

Full id: C556_pharyngeal_Gingival_Retinal_lung_Mallassezderived_Small_mesothelioma

Phase1 CAGE Peaks

Hg19::chr11:102642814..102642823,-	p@chr11:102642814..102642823 -
Hg19::chr11:102651279..102651288,-	p2@MMP10
Hg19::chr11:102651343..102651365,-	p1@MMP10
Hg19::chr11:102700844..102700849,-	p@chr11:102700844..102700849 -
Hg19::chr14:22659199..22659211,-	p@chr14:22659199..22659211 -
Hg19::chr14:22677969..22677976,-	p@chr14:22677969..22677976 -
Hg19::chr14:22678054..22678089,-	p@chr14:22678054..22678089 -
Hg19::chr14:22678115..22678119,-	p@chr14:22678115..22678119 -
Hg19::chr16:23119386..23119416,-	p@chr16:23119386..23119416 -
Hg19::chr1:211565263..211565280,+	p@chr1:211565263..211565280 +
Hg19::chr20:52771475..52771478,-	p@chr20:52771475..52771478 -
Hg19::chr20:52790360..52790374,-	p2@CYP24A1
Hg19::chr20:52790516..52790531,-	p1@CYP24A1
Hg19::chr20:52790691..52790695,-	p5@CYP24A1
Hg19::chr5:170179543..170179549,+	p@chr5:170179543..170179549 +
Hg19::chr8:61167556..61167596,-	p@chr8:61167556..61167596 -

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:0030342	1-alpha,25-dihydroxyvitamin D3 (1,25-(OH)2D3) 24-hydroxylase activity	0.0016484163428706
GO:0030303	stromelysin 2 activity	0.0016484163428706
GO:0030574	collagen catabolic process	0.00689114531961418
GO:0044256	protein digestion	0.00689114531961418
GO:0044254	multicellular organismal protein catabolic process	0.00689114531961418
GO:0044266	multicellular organismal macromolecule catabolic process	0.00689114531961418
GO:0044259	multicellular organismal macromolecule metabolic process	0.00689114531961418
GO:0044268	multicellular organismal protein metabolic process	0.00689114531961418
GO:0032963	collagen metabolic process	0.00689114531961418
GO:0044243	multicellular organismal catabolic process	0.00689114531961418
GO:0044236	multicellular organismal metabolic process	0.00689114531961418
GO:0007586	digestion	0.0260638153203052

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
epithelial cell	6.90e-27	254
squamous epithelial cell	2.14e-14	62
embryonic cell	2.07e-11	248
endothelial cell of vascular tree	4.63e-11	24
endo-epithelial cell	2.69e-10	43
endodermal cell	9.51e-09	59
blood vessel endothelial cell	1.17e-08	18
embryonic blood vessel endothelial progenitor cell	1.17e-08	18
lining cell	3.29e-08	57
barrier cell	3.29e-08	57
respiratory epithelial cell	8.12e-08	13
endothelial cell	1.67e-07	35

Uber Anatomy

Ontology term	p-value	n
multi-cellular organism	1.71e-15	659
anatomical system	3.78e-15	625
anatomical group	6.66e-15	626
embryo	3.87e-11	612
germ layer	4.01e-11	604
embryonic tissue	4.01e-11	604
presumptive structure	4.01e-11	604
epiblast (generic)	4.01e-11	604
embryonic structure	6.49e-11	605
developing anatomical structure	6.49e-11	605
vessel	2.06e-10	69
endoderm-derived structure	3.94e-10	169
endoderm	3.94e-10	169
presumptive endoderm	3.94e-10	169
blood vessel	7.05e-10	60
epithelial tube open at both ends	7.05e-10	60
blood vasculature	7.05e-10	60
vascular cord	7.05e-10	60
splanchnic layer of lateral plate mesoderm	2.59e-09	84
epithelial tube	2.81e-09	118
vasculature	5.88e-09	79
vascular system	5.88e-09	79
endo-epithelium	9.05e-09	82
endothelium	1.17e-08	18
blood vessel endothelium	1.17e-08	18
cardiovascular system endothelium	1.17e-08	18
female organism	1.61e-08	41
artery	2.05e-08	42
arterial blood vessel	2.05e-08	42
arterial system	2.05e-08	42
anatomical conduit	2.76e-08	241
simple squamous epithelium	2.77e-08	22
female reproductive organ	1.03e-07	37
female reproductive system	1.03e-07	37
organ	1.84e-07	511
systemic artery	2.74e-07	33
systemic arterial system	2.74e-07	33
epithelium	3.77e-07	309
unilaminar epithelium	4.53e-07	138
thoracic segment of trunk	4.97e-07	52
respiratory system	5.49e-07	72
digestive system	6.82e-07	155
digestive tract	6.82e-07	155
primitive gut	6.82e-07	155
cell layer	7.69e-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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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.