Coexpression cluster:C666

Full id: C666_tenocyte_Synoviocyte_Fibroblast_Chondrocyte_Nucleus_normal_mesenchymal

Phase1 CAGE Peaks

Hg19::chr1:56962127..56962135,-	p@chr1:56962127..56962135 -
Hg19::chr1:56962213..56962224,-	p@chr1:56962213..56962224 -
Hg19::chr1:56977768..56977801,-	p@chr1:56977768..56977801 -
Hg19::chr1:56977818..56977827,-	p@chr1:56977818..56977827 -
Hg19::chr1:56990054..56990076,-	p@chr1:56990054..56990076 -
Hg19::chr1:56990149..56990181,-	p@chr1:56990149..56990181 -
Hg19::chr1:56990206..56990220,-	p@chr1:56990206..56990220 -
Hg19::chr1:57044697..57044720,-	p9@PPAP2B
Hg19::chr1:57044945..57044953,-	p13@PPAP2B
Hg19::chr1:57044980..57045112,-	p1@PPAP2B
Hg19::chr1:57045115..57045143,-	p6@PPAP2B
Hg19::chr1:57045207..57045226,-	p2@PPAP2B
Hg19::chr1:57045228..57045242,-	p3@PPAP2B

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
fibroblast	2.40e-11	76
skin fibroblast	3.83e-10	23
fat cell	3.89e-08	15

Uber Anatomy

Ontology term	p-value	n
adult organism	6.89e-22	114
multi-cellular organism	4.14e-11	656
structure with developmental contribution from neural crest	1.37e-10	132
neural tube	2.44e-10	56
neural rod	2.44e-10	56
future spinal cord	2.44e-10	56
neural keel	2.44e-10	56
brain grey matter	2.81e-09	34
gray matter	2.81e-09	34
regional part of nervous system	3.65e-09	53
regional part of brain	3.65e-09	53
telencephalon	4.60e-09	34
central nervous system	1.12e-08	81
regional part of telencephalon	1.27e-08	32
cerebral hemisphere	1.28e-08	32
surface structure	2.22e-08	99
organ	2.43e-08	503
regional part of forebrain	8.61e-08	41
forebrain	8.61e-08	41
anterior neural tube	8.61e-08	41
future forebrain	8.61e-08	41
anatomical system	9.04e-08	624
neural plate	9.21e-08	82
presumptive neural plate	9.21e-08	82
anatomical group	1.15e-07	625
integument	1.25e-07	46
integumental system	1.25e-07	46
multi-tissue structure	1.93e-07	342
brain	2.60e-07	68
future brain	2.60e-07	68
skin of body	2.97e-07	41
neurectoderm	8.05e-07	86

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
REST#5978	6	4.4538594074437	0.00111223676696847	0.00772141024364667
SMC3#9126	5	5.78651263266648	0.00106075295019698	0.00749502586872485
TAF7#6879	6	5.27680126381104	0.000446292320197271	0.00415384757410951
TCF7L2#6934	5	4.14237560120667	0.00468850344400493	0.022119646347221
ZNF263#10127	6	3.79469614015877	0.00258517358054671	0.0142989589862683

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.