Coexpression cluster:C1671

Full id: C1671_Alveolar_Mesenchymal_Renal_Pericytes_Fibroblast_Placental_Smooth

Phase1 CAGE Peaks

Hg19::chr12:49961883..49961933,-	p1@MCRS1
Hg19::chr17:80009748..80009808,+	p1@GPS1
Hg19::chr19:52693259..52693335,+	p1@PPP2R1A
Hg19::chr8:144911476..144911517,-	p1@PUF60
Hg19::chr9:131873659..131873703,+	p1@PPP2R4

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
0.00011825831370825	0.0249525041924409	2	99	IL-6 Signaling Pathway (Wikipathways):WP364
0.00011825831370825	0.0249525041924409	2	99	Wnt Signaling Pathway and Pluripotency (Wikipathways):WP399
1.54262472139839e-05	0.00976481448645182	2	36	Glycogen Metabolism (Wikipathways):WP500

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:0043086	negative regulation of catalytic activity	3.78194462493104e-05
GO:0045936	negative regulation of phosphate metabolic process	0.000158051900403208
GO:0000188	inactivation of MAPK activity	0.000206622407020211
GO:0043407	negative regulation of MAP kinase activity	0.000279449198969006
GO:0000159	protein phosphatase type 2A complex	0.000401363718236737
GO:0008601	protein phosphatase type 2A regulator activity	0.000401363718236737
GO:0008287	protein serine/threonine phosphatase complex	0.000691525695820129
GO:0006469	negative regulation of protein kinase activity	0.000691525695820129
GO:0033673	negative regulation of kinase activity	0.000691525695820129
GO:0051348	negative regulation of transferase activity	0.000691525695820129
GO:0051174	regulation of phosphorus metabolic process	0.000789676369929298
GO:0019220	regulation of phosphate metabolic process	0.000789676369929298
GO:0019888	protein phosphatase regulator activity	0.000893608372889712
GO:0050790	regulation of catalytic activity	0.000893608372889712
GO:0019208	phosphatase regulator activity	0.000893608372889712
GO:0043405	regulation of MAP kinase activity	0.00102509877655625
GO:0065009	regulation of a molecular function	0.00102509877655625
GO:0051248	negative regulation of protein metabolic process	0.00115829653005875
GO:0046982	protein heterodimerization activity	0.00115829653005875
GO:0032516	positive regulation of phosphoprotein phosphatase activity	0.00149739683319767
GO:0035305	negative regulation of dephosphorylation	0.00149739683319767
GO:0035308	negative regulation of protein amino acid dephosphorylation	0.00149739683319767
GO:0032515	negative regulation of phosphoprotein phosphatase activity	0.00149739683319767
GO:0000165	MAPKKK cascade	0.00187182064475157
GO:0043234	protein complex	0.00225849552721242
GO:0008160	protein tyrosine phosphatase activator activity	0.00237504134788093
GO:0035304	regulation of protein amino acid dephosphorylation	0.00237504134788093
GO:0035306	positive regulation of dephosphorylation	0.00237504134788093
GO:0035307	positive regulation of protein amino acid dephosphorylation	0.00237504134788093
GO:0044428	nuclear part	0.00256907040405961
GO:0008380	RNA splicing	0.00322838175416037
GO:0051004	regulation of lipoprotein lipase activity	0.00322838175416037
GO:0005625	soluble fraction	0.00328201699106695
GO:0045859	regulation of protein kinase activity	0.00328201699106695
GO:0043549	regulation of kinase activity	0.00328201699106695
GO:0006470	protein amino acid dephosphorylation	0.00328201699106695
GO:0051338	regulation of transferase activity	0.00328201699106695
GO:0051721	protein phosphatase 2A binding	0.00335941899159541
GO:0050732	negative regulation of peptidyl-tyrosine phosphorylation	0.00335941899159541
GO:0042518	negative regulation of tyrosine phosphorylation of Stat3 protein	0.00335941899159541
GO:0042532	negative regulation of tyrosine phosphorylation of STAT protein	0.00335941899159541
GO:0016311	dephosphorylation	0.00371002105991095
GO:0046426	negative regulation of JAK-STAT cascade	0.00391272925030626
GO:0035303	regulation of dephosphorylation	0.00391272925030626
GO:0032991	macromolecular complex	0.00402677508269199
GO:0051346	negative regulation of hydrolase activity	0.00439531790564664
GO:0019907	cyclin-dependent protein kinase activating kinase holoenzyme complex	0.00439531790564664
GO:0046983	protein dimerization activity	0.00537789962602607
GO:0033239	negative regulation of amine metabolic process	0.00537789962602607
GO:0001933	negative regulation of protein amino acid phosphorylation	0.00537789962602607
GO:0045763	negative regulation of amino acid metabolic process	0.00537789962602607
GO:0007243	protein kinase cascade	0.00537789962602607
GO:0031324	negative regulation of cellular metabolic process	0.00541627948881933
GO:0005515	protein binding	0.0055324140350824
GO:0008180	signalosome	0.0055324140350824
GO:0042516	regulation of tyrosine phosphorylation of Stat3 protein	0.0055324140350824
GO:0042503	tyrosine phosphorylation of Stat3 protein	0.0059348073943482
GO:0005095	GTPase inhibitor activity	0.0059348073943482
GO:0051246	regulation of protein metabolic process	0.00595602286000441
GO:0009892	negative regulation of metabolic process	0.00610674870586535
GO:0043666	regulation of phosphoprotein phosphatase activity	0.00610674870586535
GO:0019211	phosphatase activator activity	0.00610674870586535
GO:0042326	negative regulation of phosphorylation	0.00655577712693528
GO:0042509	regulation of tyrosine phosphorylation of STAT protein	0.00699071010828025
GO:0046425	regulation of JAK-STAT cascade	0.00794117338964218
GO:0006396	RNA processing	0.00819423571368854
GO:0019903	protein phosphatase binding	0.00873031183308974
GO:0007260	tyrosine phosphorylation of STAT protein	0.00910738425907021
GO:0019902	phosphatase binding	0.0109673418675596
GO:0045937	positive regulation of phosphate metabolic process	0.0122826775851395
GO:0030111	regulation of Wnt receptor signaling pathway	0.0130769167866152
GO:0006275	regulation of DNA replication	0.0131889294960938
GO:0050730	regulation of peptidyl-tyrosine phosphorylation	0.0131889294960938
GO:0005634	nucleus	0.0136970240374491
GO:0006464	protein modification process	0.0139019635560335
GO:0006672	ceramide metabolic process	0.0144746637695659
GO:0043412	biopolymer modification	0.0151993344077791
GO:0046519	sphingoid metabolic process	0.0154229990596633
GO:0007259	JAK-STAT cascade	0.0169640923904088
GO:0006915	apoptosis	0.0175839219603667
GO:0012501	programmed cell death	0.0175839219603667
GO:0018108	peptidyl-tyrosine phosphorylation	0.0175839219603667
GO:0018212	peptidyl-tyrosine modification	0.0175839219603667
GO:0065007	biological regulation	0.0175839219603667
GO:0001932	regulation of protein amino acid phosphorylation	0.0175839219603667
GO:0000267	cell fraction	0.0175839219603667
GO:0033238	regulation of amine metabolic process	0.0175839219603667
GO:0006521	regulation of amino acid metabolic process	0.0175839219603667
GO:0008219	cell death	0.0175839219603667
GO:0016265	death	0.0175839219603667
GO:0051052	regulation of DNA metabolic process	0.0184923501563252
GO:0048522	positive regulation of cellular process	0.0189376544774643
GO:0030308	negative regulation of cell growth	0.0195671720898842
GO:0045792	negative regulation of cell size	0.0197231137967106
GO:0044424	intracellular part	0.0198778405874726
GO:0045926	negative regulation of growth	0.0218066619643468
GO:0010033	response to organic substance	0.0218919223482464
GO:0048518	positive regulation of biological process	0.0218919223482464
GO:0042325	regulation of phosphorylation	0.0221818958115347
GO:0007254	JNK cascade	0.0223018899835282
GO:0030155	regulation of cell adhesion	0.0224194681089413
GO:0031098	stress-activated protein kinase signaling pathway	0.0226476577150369
GO:0006665	sphingolipid metabolic process	0.0226476577150369
GO:0048523	negative regulation of cellular process	0.0235410929670742
GO:0051345	positive regulation of hydrolase activity	0.0248182608014528
GO:0048519	negative regulation of biological process	0.0248950097654811
GO:0043283	biopolymer metabolic process	0.0265148531260851
GO:0048468	cell development	0.0267244856626852
GO:0051247	positive regulation of protein metabolic process	0.0267244856626852
GO:0031323	regulation of cellular metabolic process	0.0275270140054957
GO:0044446	intracellular organelle part	0.0310106326982573
GO:0044422	organelle part	0.0310106326982573
GO:0019222	regulation of metabolic process	0.0311549359038064
GO:0009968	negative regulation of signal transduction	0.0312291095401296
GO:0005622	intracellular	0.0330791608794974
GO:0018193	peptidyl-amino acid modification	0.0356717009529934
GO:0043231	intracellular membrane-bound organelle	0.0357841435503027
GO:0043227	membrane-bound organelle	0.0357841435503027
GO:0045595	regulation of cell differentiation	0.0412638299707287
GO:0016055	Wnt receptor signaling pathway	0.0412638299707287
GO:0006793	phosphorus metabolic process	0.0432363809675238
GO:0006796	phosphate metabolic process	0.0432363809675238
GO:0042803	protein homodimerization activity	0.0438331172398033
GO:0001558	regulation of cell growth	0.0445698769321459
GO:0006261	DNA-dependent DNA replication	0.0450241300018458
GO:0048869	cellular developmental process	0.0469299736103358
GO:0030154	cell differentiation	0.0469299736103358
GO:0003823	antigen binding	0.0471333021701575

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
embryonic cell	3.74e-27	248
mesodermal cell	3.68e-20	119
non-terminally differentiated cell	2.77e-19	180
contractile cell	2.77e-16	59
animal cell	4.80e-16	679
eukaryotic cell	4.80e-16	679
electrically responsive cell	2.83e-15	60
electrically active cell	2.83e-15	60
epithelial cell	1.15e-13	254
muscle cell	1.57e-13	54
smooth muscle cell	3.12e-13	42
smooth muscle myoblast	3.12e-13	42
muscle precursor cell	3.68e-13	57
myoblast	3.68e-13	57
multi-potent skeletal muscle stem cell	3.68e-13	57
vascular associated smooth muscle cell	5.47e-11	32
somatic cell	3.22e-10	591
native cell	4.26e-10	722
epithelial cell of nephron	2.57e-08	16
lining cell	1.13e-07	57
barrier cell	1.13e-07	57
ectodermal cell	4.03e-07	71
kidney cortical cell	4.28e-07	13
renal cortical epithelial cell	4.28e-07	13

Uber Anatomy

Ontology term	p-value	n
cell layer	3.50e-15	312
dermomyotome	1.75e-14	70
epithelium	2.12e-14	309
epithelial tube	2.78e-14	118
multilaminar epithelium	3.06e-14	82
vasculature	4.55e-14	79
vascular system	4.55e-14	79
somite	7.81e-14	83
paraxial mesoderm	7.81e-14	83
presomitic mesoderm	7.81e-14	83
presumptive segmental plate	7.81e-14	83
trunk paraxial mesoderm	7.81e-14	83
presumptive paraxial mesoderm	7.81e-14	83
artery	4.95e-13	42
arterial blood vessel	4.95e-13	42
arterial system	4.95e-13	42
splanchnic layer of lateral plate mesoderm	2.18e-12	84
skeletal muscle tissue	4.57e-12	61
striated muscle tissue	4.57e-12	61
myotome	4.57e-12	61
trunk mesenchyme	5.00e-12	143
unilaminar epithelium	1.06e-11	138
blood vessel	1.74e-11	60
epithelial tube open at both ends	1.74e-11	60
blood vasculature	1.74e-11	60
vascular cord	1.74e-11	60
vessel	3.54e-11	69
muscle tissue	4.85e-11	63
musculature	4.85e-11	63
musculature of body	4.85e-11	63
circulatory system	3.09e-09	113
multi-tissue structure	3.21e-09	347
systemic artery	3.90e-09	33
systemic arterial system	3.90e-09	33
cardiovascular system	1.20e-08	110
nephron epithelium	2.57e-08	16
nephron	2.57e-08	16
uriniferous tubule	2.57e-08	16
metanephric mesenchyme	2.57e-08	16
nephrogenic mesenchyme	2.57e-08	16
anatomical cluster	3.22e-08	286
mesenchyme	7.19e-08	238
entire embryonic mesenchyme	7.19e-08	238
organism subdivision	7.66e-08	365
trunk	8.19e-08	216
tube	1.37e-07	194
excretory tube	1.69e-07	17
mesonephric epithelium	1.69e-07	17
mesonephric tubule	1.69e-07	17
nephric duct	1.69e-07	17
kidney epithelium	1.69e-07	17
renal duct	1.69e-07	17
mesonephric duct	1.69e-07	17
pronephric duct	1.69e-07	17
cortex of kidney	4.28e-07	13
renal parenchyma	4.28e-07	13

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.