Coexpression cluster:C536

Full id: C536_Chondrocyte_Mallassezderived_liver_mesothelioma_Adipocyte_serous_tenocyte

Phase1 CAGE Peaks

Hg19::chr11:73003801..73003812,+	p5@P2RY6
Hg19::chr11:73003824..73003859,+	p4@P2RY6
Hg19::chr12:54651599..54651610,-	p40@CBX5
Hg19::chr12:57629258..57629306,-	p@chr12:57629258..57629306 -
Hg19::chr1:172224417..172224440,+	p@chr1:172224417..172224440 +
Hg19::chr1:172224446..172224459,+	p@chr1:172224446..172224459 +
Hg19::chr1:186265353..186265386,+	p2@PRG4
Hg19::chr1:186265399..186265414,+	p3@PRG4
Hg19::chr1:186265958..186265975,+	p1@PRG4
Hg19::chr1:186275480..186275498,+	p@chr1:186275480..186275498 +
Hg19::chr1:186277186..186277192,+	p@chr1:186277186..186277192 +
Hg19::chr1:203148612..203148623,-	p12@CHI3L1
Hg19::chr4:71384280..71384295,+	p1@AMTN
Hg19::chr4:71384300..71384314,+	p2@AMTN
Hg19::chr6:44192182..44192212,+	p@chr6:44192182..44192212 +
Hg19::chr7:138440637..138440651,-	p6@ATP6V0A4
Hg19::chr8:37535618..37535621,+	p@chr8:37535618..37535621 +

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

---

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

---

GO ID	GO name	FDR corrected p-value
GO:0001503	ossification	0.00640592717668816
GO:0031214	biomineral formation	0.00640592717668816
GO:0046849	bone remodeling	0.00640592717668816
GO:0048771	tissue remodeling	0.00640592717668816
GO:0045029	UDP-activated nucleotide receptor activity	0.0109394665143773
GO:0044421	extracellular region part	0.0109394665143773
GO:0015065	uridine nucleotide receptor activity	0.0112417520314546
GO:0010369	chromocenter	0.0112417520314546
GO:0001501	skeletal development	0.0112417520314546
GO:0009888	tissue development	0.0187424580794987
GO:0033176	proton-transporting V-type ATPase complex	0.0187424580794987
GO:0016471	vacuolar proton-transporting V-type ATPase complex	0.0187424580794987
GO:0030321	transepithelial chloride transport	0.0197708084273638
GO:0031526	brush border membrane	0.020651913924604
GO:0031253	cell projection membrane	0.0209419681294724
GO:0005720	nuclear heterochromatin	0.0209419681294724
GO:0005578	proteinaceous extracellular matrix	0.0209419681294724
GO:0006032	chitin catabolic process	0.0209419681294724
GO:0006046	N-acetylglucosamine catabolic process	0.0209419681294724
GO:0006043	glucosamine catabolic process	0.0209419681294724
GO:0046348	amino sugar catabolic process	0.0209419681294724
GO:0006030	chitin metabolic process	0.0209419681294724
GO:0004568	chitinase activity	0.0209419681294724
GO:0042475	odontogenesis of dentine-containing teeth	0.0240726321286024
GO:0005615	extracellular space	0.0240726321286024
GO:0000792	heterochromatin	0.0240726321286024
GO:0044247	cellular polysaccharide catabolic process	0.0240726321286024
GO:0000272	polysaccharide catabolic process	0.0240726321286024
GO:0000790	nuclear chromatin	0.0246039581569741
GO:0005903	brush border	0.0246039581569741
GO:0042476	odontogenesis	0.0258769327209588
GO:0044459	plasma membrane part	0.02962117468154
GO:0000776	kinetochore	0.0301294004526983
GO:0006885	regulation of pH	0.0311253213876219
GO:0006044	N-acetylglucosamine metabolic process	0.0311499775159384
GO:0006041	glucosamine metabolic process	0.0311731329495279
GO:0005605	basal lamina	0.0327877433031848
GO:0006040	amino sugar metabolic process	0.0327877433031848
GO:0007588	excretion	0.0327877433031848
GO:0045028	purinergic nucleotide receptor activity, G-protein coupled	0.0327877433031848
GO:0001608	nucleotide receptor activity, G-protein coupled	0.0327877433031848
GO:0016502	nucleotide receptor activity	0.0327877433031848
GO:0001614	purinergic nucleotide receptor activity	0.0327877433031848
GO:0044463	cell projection part	0.0342197334329908
GO:0016020	membrane	0.035877530424629
GO:0005774	vacuolar membrane	0.0431306493098143
GO:0044437	vacuolar part	0.0435682734962295
GO:0044454	nuclear chromosome part	0.0443887852564877
GO:0016324	apical plasma membrane	0.0443887852564877
GO:0005604	basement membrane	0.0473184421331456
GO:0000775	chromosome, pericentric region	0.0476374206378702
GO:0044264	cellular polysaccharide metabolic process	0.0493340200671556
GO:0005976	polysaccharide metabolic process	0.0493340200671556
GO:0045177	apical part of cell	0.0493340200671556
GO:0006821	chloride transport	0.0493340200671556
GO:0007200	G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)	0.0493340200671556
GO:0048513	organ development	0.0493340200671556

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>

---

Cell Type

Ontology term	p-value	n
GAG secreting cell	5.88e-45	9
carbohydrate secreting cell	5.88e-45	9
collagen secreting cell	1.32e-30	6
chondroblast	1.32e-30	6
chondrocyte	1.32e-30	6
extracellular matrix secreting cell	6.84e-27	15
stromal cell	3.29e-19	28
synovial cell	4.30e-16	3
secretory cell	5.23e-11	36

Uber Anatomy

Ontology term	p-value	n
stratified squamous epithelium	4.30e-16	3
layer of synovial tissue	4.30e-16	3
synovial joint	4.30e-16	3
synovial membrane of synovial joint	4.30e-16	3
dura mater	3.45e-12	1
future meninx	3.45e-12	1
ectomeninx	3.45e-12	1
future dura mater	3.45e-12	1
open tracheal system trachea	9.54e-07	2

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

---

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

---

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

---

This analysis result is provided for C0 - C305 clusters.