Coexpression cluster:C283

Full id: C283_tenocyte_Chondrocyte_mesenchymal_Macrophage_pleomorphic_Synoviocyte_cholangiocellular

Phase1 CAGE Peaks

Hg19::chr1:203148057..203148072,+	p@chr1:203148057..203148072 +
Hg19::chr1:203148146..203148212,+	p1@CU678996
Hg19::chr1:203148270..203148291,-	p@chr1:203148270..203148291 -
Hg19::chr1:203148271..203148296,+	p7@CU678996
Hg19::chr1:203148336..203148348,-	p@chr1:203148336..203148348 -
Hg19::chr1:203148357..203148383,-	p@chr1:203148357..203148383 -
Hg19::chr1:203148373..203148396,+	p3@CU678996
Hg19::chr1:203148394..203148401,-	p10@CHI3L1
Hg19::chr1:203148408..203148431,+	p2@CU678996
Hg19::chr1:203148428..203148437,-	p11@CHI3L1
Hg19::chr1:203148455..203148477,-	p5@CHI3L1
Hg19::chr1:203148495..203148505,-	p13@CHI3L1
Hg19::chr1:203148522..203148550,-	p4@CHI3L1
Hg19::chr1:203148531..203148567,+	p4@CU678996
Hg19::chr1:203148907..203148922,+	p@chr1:203148907..203148922 +
Hg19::chr1:203148919..203148937,-	p16@CHI3L1
Hg19::chr1:203148938..203148988,-	p6@CHI3L1
Hg19::chr1:203149716..203149729,-	p19@CHI3L1
Hg19::chr1:203149741..203149762,-	p14@CHI3L1
Hg19::chr1:203149809..203149816,-	p@chr1:203149809..203149816 -
Hg19::chr1:203150031..203150040,-	p@chr1:203150031..203150040 -
Hg19::chr1:203150041..203150049,-	p@chr1:203150041..203150049 -
Hg19::chr1:203150369..203150408,-	p@chr1:203150369..203150408 -
Hg19::chr1:203151897..203151908,-	p15@CHI3L1
Hg19::chr1:203151934..203151947,-	p7@CHI3L1
Hg19::chr1:203151964..203151973,-	p21@CHI3L1
Hg19::chr1:203152777..203152814,+	p@chr1:203152777..203152814 +
Hg19::chr1:203152791..203152804,-	p@chr1:203152791..203152804 -
Hg19::chr1:203152808..203152846,-	p@chr1:203152808..203152846 -
Hg19::chr1:203152845..203152866,+	p@chr1:203152845..203152866 +
Hg19::chr1:203152849..203152863,-	p@chr1:203152849..203152863 -
Hg19::chr1:203152872..203152879,-	p@chr1:203152872..203152879 -
Hg19::chr1:203152908..203152924,-	p@chr1:203152908..203152924 -
Hg19::chr1:203153416..203153419,-	p@chr1:203153416..203153419 -
Hg19::chr1:203153711..203153722,+	p@chr1:203153711..203153722 +
Hg19::chr1:203154299..203154330,+	p@chr1:203154299..203154330 +
Hg19::chr1:203154334..203154339,+	p@chr1:203154334..203154339 +
Hg19::chr1:203154342..203154363,-	p9@CHI3L1
Hg19::chr1:203154349..203154356,+	p@chr1:203154349..203154356 +
Hg19::chr1:203154383..203154466,-	p3@CHI3L1
Hg19::chr1:203154393..203154416,+	p@chr1:203154393..203154416 +
Hg19::chr1:203154486..203154506,-	p8@CHI3L1
Hg19::chr1:203154508..203154518,-	p20@CHI3L1
Hg19::chr1:203155464..203155497,-	p@chr1:203155464..203155497 -
Hg19::chr1:203155823..203155838,-	p1@CHI3L1
Hg19::chr1:203155868..203155882,-	p2@CHI3L1

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:0006032	chitin catabolic process	0.00331155068880254
GO:0006046	N-acetylglucosamine catabolic process	0.00331155068880254
GO:0006043	glucosamine catabolic process	0.00331155068880254
GO:0046348	amino sugar catabolic process	0.00331155068880254
GO:0006030	chitin metabolic process	0.00331155068880254
GO:0004568	chitinase activity	0.00331155068880254
GO:0044247	cellular polysaccharide catabolic process	0.00347712822324267
GO:0000272	polysaccharide catabolic process	0.00347712822324267
GO:0006044	N-acetylglucosamine metabolic process	0.00463617096432356
GO:0006041	glucosamine metabolic process	0.00463617096432356
GO:0006040	amino sugar metabolic process	0.00493722102694197
GO:0044264	cellular polysaccharide metabolic process	0.00876287259190826
GO:0005976	polysaccharide metabolic process	0.00876287259190826
GO:0005201	extracellular matrix structural constituent	0.0116377352777918
GO:0044275	cellular carbohydrate catabolic process	0.0149604172294138
GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	0.0149604172294138
GO:0016052	carbohydrate catabolic process	0.0149604172294138
GO:0016798	hydrolase activity, acting on glycosyl bonds	0.0161898033674791
GO:0005529	sugar binding	0.0241917492424101
GO:0005578	proteinaceous extracellular matrix	0.0278832567997174
GO:0043285	biopolymer catabolic process	0.0279759802190039
GO:0030246	carbohydrate binding	0.0279759802190039
GO:0044262	cellular carbohydrate metabolic process	0.0279759802190039
GO:0044265	cellular macromolecule catabolic process	0.0279759802190039
GO:0005615	extracellular space	0.0279759802190039
GO:0009057	macromolecule catabolic process	0.0312021664900506
GO:0009308	amine metabolic process	0.0312021664900506
GO:0006807	nitrogen compound metabolic process	0.0320747338144018
GO:0005975	carbohydrate metabolic process	0.0357205934298834
GO:0044248	cellular catabolic process	0.0357205934298834
GO:0044421	extracellular region part	0.0388840145394879
GO:0009056	catabolic process	0.0402767352525609

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
adult organism	1.41e-29	115
neural tube	2.67e-15	57
neural rod	2.67e-15	57
future spinal cord	2.67e-15	57
neural keel	2.67e-15	57
central nervous system	5.95e-14	82
regional part of brain	3.09e-12	59
anterior neural tube	3.15e-12	42
brain	4.41e-12	69
future brain	4.41e-12	69
regional part of nervous system	4.42e-12	94
nervous system	4.42e-12	94
regional part of forebrain	5.92e-12	41
forebrain	5.92e-12	41
future forebrain	5.92e-12	41
neural plate	6.65e-10	86
presumptive neural plate	6.65e-10	86
gray matter	9.06e-10	34
brain grey matter	9.06e-10	34
telencephalon	2.23e-09	34
regional part of telencephalon	4.13e-09	33
neurectoderm	6.14e-09	90
cerebral hemisphere	1.44e-08	32
tissue	1.16e-07	787
pre-chordal neural plate	6.77e-07	61

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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