Coexpression cluster:C383

Full id: C383_oral_liposarcoma_small_Small_skeletal_amniotic_Astrocyte

Phase1 CAGE Peaks

Hg19::chr10:99400163..99400169,-	p@chr10:99400163..99400169 -
Hg19::chr11:30496173..30496192,+	p@chr11:30496173..30496192 +
Hg19::chr11:30496199..30496218,+	p@chr11:30496199..30496218 +
Hg19::chr17:70680022..70680046,-	p@chr17:70680022..70680046 -
Hg19::chr18:3602688..3602692,+	p1@MGC11082
Hg19::chr20:23120219..23120223,-	p@chr20:23120219..23120223 -
Hg19::chr2:120974061..120974068,-	p3@ENST00000455707
Hg19::chr2:209003854..209003858,-	p@chr2:209003854..209003858 -
Hg19::chr3:54660709..54660712,-	p@chr3:54660709..54660712 -
Hg19::chr6:102844491..102844494,+	p@chr6:102844491..102844494 +
Hg19::chr6:123728153..123728175,-	p@chr6:123728153..123728175 -
Hg19::chr6:125186828..125186832,+	p@chr6:125186828..125186832 +
Hg19::chr6:125283093..125283144,+	p@chr6:125283093..125283144 +
Hg19::chr6:125283157..125283197,+	p1@RNF217
Hg19::chr6:125283201..125283226,+	p6@RNF217
Hg19::chr6:125283242..125283303,+	p2@RNF217
Hg19::chr6:125283415..125283431,+	p7@RNF217
Hg19::chr6:125283436..125283477,+	p5@RNF217
Hg19::chr6:125284075..125284181,+	p4@RNF217
Hg19::chr6:125284314..125284343,+	p8@RNF217
Hg19::chr6:125284359..125284375,+	p9@RNF217
Hg19::chr6:125284405..125284429,-	p4@ENST00000439075
Hg19::chr6:125284416..125284459,+	p10@RNF217
Hg19::chr6:125284525..125284534,-	p8@ENST00000439075
Hg19::chr6:125284540..125284551,-	p7@ENST00000439075
Hg19::chr6:125314790..125314796,+	p@chr6:125314790..125314796 +
Hg19::chr6:125426966..125426967,+	p@chr6:125426966..125426967 +
Hg19::chr8:101661887..101661901,-	p2@SNX31

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:0042787	protein ubiquitination during ubiquitin-dependent protein catabolic process	0.00632874131637819
GO:0016567	protein ubiquitination	0.0315382275599513
GO:0032446	protein modification by small protein conjugation	0.0315382275599513
GO:0004842	ubiquitin-protein ligase activity	0.0315382275599513
GO:0008639	small protein conjugating enzyme activity	0.0315382275599513
GO:0019787	small conjugating protein ligase activity	0.0315382275599513
GO:0006511	ubiquitin-dependent protein catabolic process	0.0315382275599513
GO:0043632	modification-dependent macromolecule catabolic process	0.0315382275599513
GO:0019941	modification-dependent protein catabolic process	0.0315382275599513
GO:0051603	proteolysis involved in cellular protein catabolic process	0.0315382275599513
GO:0044257	cellular protein catabolic process	0.0315382275599513
GO:0016881	acid-amino acid ligase activity	0.0315382275599513
GO:0030163	protein catabolic process	0.0335423289768044
GO:0016879	ligase activity, forming carbon-nitrogen bonds	0.0335423289768044
GO:0043285	biopolymer catabolic process	0.038309980768476
GO:0044265	cellular macromolecule catabolic process	0.0408762233257838
GO:0006512	ubiquitin cycle	0.0408762233257838
GO:0009057	macromolecule catabolic process	0.0431020592810178
GO:0016874	ligase activity	0.0431020592810178

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
bladder cell	1.43e-10	1
lower urinary tract cell	1.43e-10	1

Uber Anatomy

Ontology term	p-value	n
urinary bladder urothelium	1.43e-10	1
wall of urinary bladder	1.43e-10	1
mucosa of urinary bladder	1.43e-10	1
mucosa of oral region	1.90e-10	4
respiratory system mucosa	1.90e-10	4
mammalian vulva	2.28e-10	1
external female genitalia	2.28e-10	1

Disease

Ontology term	p-value	n
squamous cell carcinoma	6.86e-11	14
skin squamous cell carcinoma	4.33e-10	1
keratoacanthoma	4.33e-10	1
carcinoma	3.58e-07	106

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
CCNT2#905	12	2.71551496155541	0.000597889218674049	0.00499663536121461
CTCF#10664	11	2.10581500370805	0.0088321798606111	0.0335329370533068
CTCFL#140690	6	4.23138736263736	0.00241671280905517	0.0136188997499009
GATA3#2625	5	4.86366363521536	0.00322975720817582	0.0167326064320985
RAD21#5885	8	2.95858111298752	0.00399330723101714	0.019150381756828
TRIM28#10155	7	4.64763126131563	0.000564632721851303	0.00481739047769204

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.