Coexpression cluster:C1962

Full id: C1962_Adipocyte_Synoviocyte_Mast_mature_tenocyte_Chondrocyte_leiomyoblastoma

Phase1 CAGE Peaks

Hg19::chr5:54721817..54721840,-	p@chr5:54721817..54721840 -
Hg19::chr5:54771166..54771206,+	p@chr5:54771166..54771206 +
Hg19::chr5:54830488..54830506,-	p2@RNF138P1
Hg19::chr5:54830511..54830588,-	p1@RNF138P1
Hg19::chr5:54830784..54830799,-	p1@PPAP2A

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:0008195	phosphatidate phosphatase activity	0.0139516400949588
GO:0008354	germ cell migration	0.0139516400949588
GO:0046839	phospholipid dephosphorylation	0.028399509486818
GO:0019216	regulation of lipid metabolic process	0.028399509486818
GO:0030521	androgen receptor signaling pathway	0.028399509486818
GO:0007205	protein kinase C activation	0.028399509486818
GO:0030518	steroid hormone receptor signaling pathway	0.028399509486818
GO:0030258	lipid modification	0.028399509486818
GO:0030522	intracellular receptor-mediated signaling pathway	0.028399509486818
GO:0032147	activation of protein kinase activity	0.0325231595799832
GO:0007200	G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)	0.0371594678851849
GO:0048015	phosphoinositide-mediated signaling	0.0454807681646362
GO:0045860	positive regulation of protein kinase activity	0.0454807681646362
GO:0033674	positive regulation of kinase activity	0.0454807681646362
GO:0051347	positive regulation of transferase activity	0.0454807681646362

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	2.59e-12	15
fibroblast	8.47e-10	76

Uber Anatomy

Ontology term	p-value	n
adult organism	3.16e-27	114
multi-tissue structure	3.81e-12	342
neural tube	1.48e-10	56
neural rod	1.48e-10	56
future spinal cord	1.48e-10	56
neural keel	1.48e-10	56
multi-cellular organism	2.24e-10	656
structure with developmental contribution from neural crest	2.70e-10	132
anatomical cluster	6.69e-10	373
anatomical conduit	1.34e-09	240
regional part of nervous system	2.45e-09	53
regional part of brain	2.45e-09	53
central nervous system	3.76e-09	81
brain	4.44e-09	68
future brain	4.44e-09	68
primary circulatory organ	1.79e-08	27
organ system subdivision	2.69e-08	223
neural plate	7.39e-08	82
presumptive neural plate	7.39e-08	82
regional part of forebrain	1.14e-07	41
forebrain	1.14e-07	41
anterior neural tube	1.14e-07	41
future forebrain	1.14e-07	41
tube	1.22e-07	192
heart	1.26e-07	24
primitive heart tube	1.26e-07	24
primary heart field	1.26e-07	24
anterior lateral plate mesoderm	1.26e-07	24
heart tube	1.26e-07	24
heart primordium	1.26e-07	24
cardiac mesoderm	1.26e-07	24
cardiogenic plate	1.26e-07	24
heart rudiment	1.26e-07	24
nervous system	1.88e-07	89
mesenchyme	2.78e-07	160
entire embryonic mesenchyme	2.78e-07	160
epithelium	6.40e-07	306
adipose tissue	7.92e-07	14

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
NR3C1#2908	3	8.98381399870382	0.00268799578894045	0.0147987133474513
TFAP2C#7022	3	6.48553716591613	0.00685895151794	0.0290664247345156

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.