Coexpression cluster:C4038

Full id: C4038_Synoviocyte_ovary_tenocyte_Nucleus_left_Mesenchymal_Pericytes

Phase1 CAGE Peaks

Hg19::chr20:43343596..43343608,+	p6@WISP2
Hg19::chr20:43343610..43343645,+	p5@WISP2
Hg19::chr20:43343646..43343655,+	p7@WISP2

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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No GOStat results

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
nucleus pulposus cell of intervertebral disc	5.46e-10	3

Uber Anatomy

Ontology term	p-value	n
articulation	6.46e-18	8
skeletal joint	6.46e-18	8
articular system	6.46e-18	8
adult organism	2.50e-15	114
intervertebral cartilage	5.82e-15	5
symphysis	5.82e-15	5
nonsynovial joint	5.82e-15	5
fibrous joint	5.82e-15	5
cartilaginous joint	5.82e-15	5
developing mesenchymal condensation	5.82e-15	5
pre-cartilage condensation	5.82e-15	5
cartilaginous condensation	5.82e-15	5
cartilage element	5.82e-15	5
post-cranial axial skeletal system	5.82e-15	5
vertebral column	5.82e-15	5
intervertebral disk	5.82e-15	5
intervertebral joint	5.82e-15	5
nucleus pulposus	5.46e-10	3
axial mesoderm	5.46e-10	3
notochord	5.46e-10	3
chordamesoderm	5.46e-10	3
valve	2.52e-09	3
cardiac mesenchyme	2.52e-09	3
cardial valve	2.52e-09	3
tunica intima	2.52e-09	3
heart layer	2.52e-09	3
endocardium	2.52e-09	3
endocardial cushion	2.52e-09	3
presumptive endocardium	2.52e-09	3
cardiac atrium	4.14e-07	2
future cardiac atrium	4.14e-07	2
atrioventricular valve	5.54e-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

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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
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115366003730574
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0325868218711633
ESR1#2099	3	30.7686032961545	3.43136389821584e-05	0.000677188613313991
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00582135535113741
FOXA2#3170	3	24.6304637526652	6.68983856509345e-05	0.00107340612981993
SMARCB1#6598	3	18.2527157811574	0.00016439776067989	0.00203334174889235
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00614546174269119
TFAP2A#7020	3	16.518634373045	0.000221803388076634	0.00248524021535625
TFAP2C#7022	3	10.8092286098602	0.000791674657575313	0.00616567558258823

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.