Coexpression cluster:C240

Full id: C240_Adipocyte_Preadipocyte_Osteoblast_Chondrocyte_tenocyte_Synoviocyte_mesenchymal

Phase1 CAGE Peaks

Hg19::chr13:114567443..114567462,-	p11@GAS6
Hg19::chr14:23080048..23080060,+	p3@ABHD4
Hg19::chr15:68643106..68643126,-	p4@ITGA11
Hg19::chr15:68653998..68654015,-	p@chr15:68653998..68654015 -
Hg19::chr19:18709616..18709634,-	p@chr19:18709616..18709634 -
Hg19::chr19:18893583..18893586,+	p@chr19:18893583..18893586 +
Hg19::chr19:18893717..18893745,+	p@chr19:18893717..18893745 +
Hg19::chr19:18893751..18893758,-	p@chr19:18893751..18893758 -
Hg19::chr19:18893910..18893932,-	p@chr19:18893910..18893932 -
Hg19::chr19:18895139..18895177,-	p@chr19:18895139..18895177 -
Hg19::chr19:18895742..18895757,-	p@chr19:18895742..18895757 -
Hg19::chr19:18895812..18895830,-	p@chr19:18895812..18895830 -
Hg19::chr19:18895892..18895911,-	p@chr19:18895892..18895911 -
Hg19::chr19:18896512..18896527,-	p@chr19:18896512..18896527 -
Hg19::chr19:18896607..18896614,-	p@chr19:18896607..18896614 -
Hg19::chr19:18896642..18896656,-	p@chr19:18896642..18896656 -
Hg19::chr19:18896798..18896823,-	p@chr19:18896798..18896823 -
Hg19::chr19:18896862..18896874,-	p@chr19:18896862..18896874 -
Hg19::chr19:18896874..18896893,+	p@chr19:18896874..18896893 +
Hg19::chr19:18896885..18896896,-	p@chr19:18896885..18896896 -
Hg19::chr19:18896916..18896933,+	p@chr19:18896916..18896933 +
Hg19::chr19:18896920..18896932,-	p@chr19:18896920..18896932 -
Hg19::chr19:18896944..18896955,-	p@chr19:18896944..18896955 -
Hg19::chr19:18897072..18897100,-	p@chr19:18897072..18897100 -
Hg19::chr19:18897375..18897390,-	p4@COMP
Hg19::chr19:18897380..18897392,+	p@chr19:18897380..18897392 +
Hg19::chr19:18897438..18897467,-	p3@COMP
Hg19::chr19:18898324..18898353,+	p@chr19:18898324..18898353 +
Hg19::chr19:18898325..18898337,-	p2@COMP
Hg19::chr19:18898355..18898369,+	p@chr19:18898355..18898369 +
Hg19::chr19:18898379..18898416,+	p@chr19:18898379..18898416 +
Hg19::chr19:18898393..18898405,-	p@chr19:18898393..18898405 -
Hg19::chr19:18898451..18898462,-	p@chr19:18898451..18898462 -
Hg19::chr19:18899076..18899101,-	p@chr19:18899076..18899101 -
Hg19::chr19:18899082..18899091,+	p@chr19:18899082..18899091 +
Hg19::chr19:18899114..18899135,-	p@chr19:18899114..18899135 -
Hg19::chr19:18899247..18899272,-	p@chr19:18899247..18899272 -
Hg19::chr19:18899276..18899289,-	p@chr19:18899276..18899289 -
Hg19::chr19:18899427..18899432,-	p@chr19:18899427..18899432 -
Hg19::chr19:18899448..18899459,-	p@chr19:18899448..18899459 -
Hg19::chr19:18899462..18899501,-	p@chr19:18899462..18899501 -
Hg19::chr19:18899504..18899530,-	p@chr19:18899504..18899530 -
Hg19::chr19:18899552..18899562,-	p@chr19:18899552..18899562 -
Hg19::chr19:18899674..18899694,-	p@chr19:18899674..18899694 -
Hg19::chr19:18899713..18899727,-	p@chr19:18899713..18899727 -
Hg19::chr19:18899991..18900007,-	p@chr19:18899991..18900007 -
Hg19::chr19:18900020..18900058,-	p@chr19:18900020..18900058 -
Hg19::chr19:18900031..18900054,+	p@chr19:18900031..18900054 +
Hg19::chr19:18900083..18900109,-	p@chr19:18900083..18900109 -
Hg19::chr19:18900774..18900802,-	p@chr19:18900774..18900802 -
Hg19::chr19:18900805..18900820,-	p@chr19:18900805..18900820 -
Hg19::chr19:18900836..18900848,-	p@chr19:18900836..18900848 -
Hg19::chr19:18900850..18900868,-	p@chr19:18900850..18900868 -
Hg19::chr19:18900893..18900901,-	p@chr19:18900893..18900901 -
Hg19::chr19:18900904..18900922,-	p@chr19:18900904..18900922 -
Hg19::chr19:18901737..18901749,-	p7@COMP
Hg19::chr22:31501005..31501034,-	p@chr22:31501005..31501034 -

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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p.value	FDR	nGenes	nPathway	Name
0.000290358189093011	0.045949183423969	2	200	Focal adhesion (KEGG):04510
5.23707650350948e-05	0.0288361706736934	2	85	ECM-receptor interaction (KEGG):04512
0.000256622577651287	0.045949183423969	2	188	Focal Adhesion (Wikipathways):WP306
9.1109543992712e-05	0.0288361706736934	3	816	TGF beta receptor up reg. targets (Netpath):NetPath_7

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:0005509	calcium ion binding	0.0232138068983212
GO:0048856	anatomical structure development	0.0268361558672058
GO:0006929	substrate-bound cell migration	0.0268361558672058
GO:0005518	collagen binding	0.0424718208543621
GO:0032502	developmental process	0.049126762771572
GO:0022610	biological adhesion	0.049126762771572
GO:0007155	cell adhesion	0.049126762771572
GO:0009653	anatomical structure morphogenesis	0.049126762771572
GO:0008305	integrin complex	0.049126762771572
GO:0048513	organ development	0.049126762771572

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
fat cell	4.49e-36	15
GAG secreting cell	8.22e-30	9
carbohydrate secreting cell	8.22e-30	9
collagen secreting cell	2.61e-23	6
chondroblast	2.61e-23	6
chondrocyte	2.61e-23	6
preadipocyte	1.21e-22	12
preadipocyte of the breast	2.06e-18	3
stromal cell	2.23e-18	28
adipocyte of omentum tissue	2.91e-18	3
fibrocyte	7.71e-18	3
attachment cell	7.71e-18	3
tendon cell	7.71e-18	3
extracellular matrix secreting cell	1.50e-17	15
omentum preadipocyte	2.02e-17	3
adipocyte of breast	5.24e-13	2
fibroblast	1.52e-11	76
mesenchymal cell	4.28e-11	354
connective tissue cell	9.33e-11	361
motile cell	1.46e-09	386
synovial cell	1.66e-08	3
subcutaneous fat cell	2.51e-08	3
multi fate stem cell	4.25e-08	427
somatic stem cell	6.77e-08	433
stem cell	1.24e-07	441
perirenal preadipocyte	4.25e-07	1
perirenal adipocyte cell	4.51e-07	1
supportive cell	5.58e-07	8
secretory cell	8.52e-07	36

Uber Anatomy

Ontology term	p-value	n
omentum	6.95e-34	6
peritoneum	6.95e-34	6
abdominal cavity	6.95e-34	6
visceral peritoneum	6.95e-34	6
cavity lining	2.94e-29	12
serous membrane	2.94e-29	12
dense regular connective tissue	7.71e-18	3
tendon	7.71e-18	3
regular connective tissue	7.71e-18	3
breast	1.03e-14	10
adipose tissue	1.06e-13	14
chest	2.37e-13	11
perirenal fat	1.67e-12	2
connective tissue	3.00e-11	371
stratified squamous epithelium	1.66e-08	3
layer of synovial tissue	1.66e-08	3
synovial joint	1.66e-08	3
synovial membrane of synovial joint	1.66e-08	3
subcutaneous adipose tissue	2.51e-08	3
mitral valve	8.49e-07	1

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
NANOG#79923	6	3.07839773484344	0.0130512135158276	0.0463025914932916
SUZ12#23512	12	10.5506907181185	1.20506169961436e-09	1.10109745272112e-07

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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