Coexpression cluster:C846

Full id: C846_pancreas_leiomyoma_Smooth_tenocyte_Fibroblast_Adipocyte_Hepatocyte

Phase1 CAGE Peaks

Hg19::chr17:79803082..79803112,-	p6@P4HB
Hg19::chr17:79803474..79803506,-	p2@P4HB
Hg19::chr17:79803795..79803822,-	p11@P4HB
Hg19::chr17:79803824..79803843,-	p18@P4HB
Hg19::chr17:79804916..79804933,-	p4@P4HB
Hg19::chr17:79804935..79804958,-	p9@P4HB
Hg19::chr17:79805146..79805197,-	p3@P4HB
Hg19::chr17:79813398..79813436,-	p5@P4HB
Hg19::chr17:79817107..79817135,-	p7@P4HB
Hg19::chr3:127783792..127783816,+	p2@SEC61A1

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
3.40211704163772e-05	0.0215354008735668	2	167	Protein processing in endoplasmic reticulum (KEGG):04141

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:0019511	peptidyl-proline hydroxylation	0.00145708230307312
GO:0018401	peptidyl-proline hydroxylation to 4-hydroxy-L-proline	0.00145708230307312
GO:0019471	4-hydroxyproline metabolic process	0.00145708230307312
GO:0018208	peptidyl-proline modification	0.00145708230307312
GO:0031545	peptidyl-proline 4-dioxygenase activity	0.00291407882225392
GO:0004656	procollagen-proline 4-dioxygenase activity	0.00291407882225392
GO:0044432	endoplasmic reticulum part	0.00330733669435169
GO:0019798	procollagen-proline dioxygenase activity	0.00437092521962316
GO:0031543	peptidyl-proline dioxygenase activity	0.00453274461806331
GO:0016864	intramolecular oxidoreductase activity, transposing S-S bonds	0.00476807149730774
GO:0003756	protein disulfide isomerase activity	0.00476807149730774
GO:0016862	intramolecular oxidoreductase activity, interconverting keto- and enol-groups	0.00485629763105131
GO:0005783	endoplasmic reticulum	0.00541052206410783
GO:0015450	P-P-bond-hydrolysis-driven protein transmembrane transporter activity	0.0100987199993063
GO:0022884	macromolecule transmembrane transporter activity	0.0100987199993063
GO:0008320	protein transmembrane transporter activity	0.0101955228325995
GO:0005793	ER-Golgi intermediate compartment	0.014238010123144
GO:0016706	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors	0.014238010123144
GO:0009306	protein secretion	0.017470575942967
GO:0005788	endoplasmic reticulum lumen	0.018261464437518
GO:0016860	intramolecular oxidoreductase activity	0.018261464437518
GO:0065002	intracellular protein transport across a membrane	0.018261464437518
GO:0048770	pigment granule	0.0201319783103799
GO:0042470	melanosome	0.0201319783103799
GO:0006575	amino acid derivative metabolic process	0.0209545000051523
GO:0045454	cell redox homeostasis	0.0241718552410727
GO:0018193	peptidyl-amino acid modification	0.0260734167618831
GO:0046483	heterocycle metabolic process	0.0270087214901337
GO:0009986	cell surface	0.0296802210019959
GO:0008565	protein transporter activity	0.02985138195407
GO:0005792	microsome	0.0303855457068317
GO:0042598	vesicular fraction	0.0307047518939551
GO:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	0.031180058507942
GO:0044446	intracellular organelle part	0.0417957995859935
GO:0044422	organelle part	0.0417957995859935
GO:0032940	secretion by cell	0.0455416090038608
GO:0015399	primary active transmembrane transporter activity	0.0455416090038608
GO:0015405	P-P-bond-hydrolysis-driven transmembrane transporter activity	0.0455416090038608
GO:0044444	cytoplasmic part	0.0455416090038608
GO:0016853	isomerase activity	0.0455416090038608
GO:0016023	cytoplasmic membrane-bound vesicle	0.0485945978872026
GO:0031988	membrane-bound vesicle	0.0485945978872026

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
animal cell	1.54e-24	679
eukaryotic cell	1.54e-24	679
somatic cell	1.72e-18	588
embryonic cell	8.27e-15	250
mesodermal cell	2.29e-14	121
fibroblast	6.90e-13	76
native cell	2.16e-12	722
muscle precursor cell	3.19e-11	58
myoblast	3.19e-11	58
multi-potent skeletal muscle stem cell	3.19e-11	58
contractile cell	5.35e-11	59
muscle cell	2.57e-10	55
smooth muscle cell	6.97e-10	43
smooth muscle myoblast	6.97e-10	43
electrically responsive cell	2.55e-09	61
electrically active cell	2.55e-09	61
epithelial cell	9.54e-09	253
vascular associated smooth muscle cell	1.67e-08	32
somatic stem cell	2.02e-08	433
multi fate stem cell	4.81e-08	427
stem cell	1.40e-07	441
non-terminally differentiated cell	5.37e-07	106

Uber Anatomy

Ontology term	p-value	n
epithelial tube	5.34e-16	117
trunk mesenchyme	4.15e-15	122
unilaminar epithelium	1.62e-13	148
trunk	2.35e-13	199
mesenchyme	7.60e-13	160
entire embryonic mesenchyme	7.60e-13	160
epithelial vesicle	9.16e-12	78
artery	1.62e-11	42
arterial blood vessel	1.62e-11	42
arterial system	1.62e-11	42
organism subdivision	2.34e-11	264
splanchnic layer of lateral plate mesoderm	2.51e-11	83
multilaminar epithelium	2.56e-10	83
skeletal muscle tissue	3.05e-10	62
striated muscle tissue	3.05e-10	62
myotome	3.05e-10	62
muscle tissue	5.51e-10	64
musculature	5.51e-10	64
musculature of body	5.51e-10	64
somite	5.86e-10	71
presomitic mesoderm	5.86e-10	71
presumptive segmental plate	5.86e-10	71
dermomyotome	5.86e-10	71
trunk paraxial mesoderm	5.86e-10	71
dense mesenchyme tissue	6.85e-10	73
vasculature	9.71e-10	78
vascular system	9.71e-10	78
vessel	1.03e-09	68
paraxial mesoderm	1.67e-09	72
presumptive paraxial mesoderm	1.67e-09	72
systemic artery	3.17e-09	33
systemic arterial system	3.17e-09	33
epithelial tube open at both ends	4.60e-09	59
blood vessel	4.60e-09	59
blood vasculature	4.60e-09	59
vascular cord	4.60e-09	59
subdivision of trunk	1.72e-07	112
surface structure	2.51e-07	99
mesoderm	2.54e-07	315
mesoderm-derived structure	2.54e-07	315
presumptive mesoderm	2.54e-07	315
circulatory system	3.95e-07	112
cardiovascular system	4.30e-07	109

Disease

Ontology term	p-value	n
ovarian cancer	1.24e-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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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

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This analysis result is provided for C0 - C305 clusters.