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	1.56e-26	250
mesodermal cell	5.52e-21	121
contractile cell	8.09e-16	59
electrically responsive cell	2.74e-15	61
electrically active cell	2.74e-15	61
non-terminally differentiated cell	2.89e-15	106
animal cell	3.93e-15	679
eukaryotic cell	3.93e-15	679
muscle cell	1.42e-13	55
smooth muscle cell	4.09e-13	43
smooth muscle myoblast	4.09e-13	43
epithelial cell	4.34e-13	253
muscle precursor cell	4.40e-13	58
myoblast	4.40e-13	58
multi-potent skeletal muscle stem cell	4.40e-13	58
vascular associated smooth muscle cell	5.06e-11	32
somatic cell	4.51e-09	588
native cell	5.97e-09	722
epithelial cell of nephron	2.22e-08	15
lining cell	2.94e-08	58
barrier cell	2.94e-08	58
kidney cortical cell	4.64e-07	12
renal cortical epithelial cell	4.64e-07	12
ectodermal cell	6.92e-07	72

Uber Anatomy

Ontology term	p-value	n
epithelial vesicle	3.58e-18	78
cell layer	9.11e-17	309
epithelium	6.00e-16	306
vasculature	4.35e-15	78
vascular system	4.35e-15	78
paraxial mesoderm	5.34e-15	72
presumptive paraxial mesoderm	5.34e-15	72
somite	6.46e-15	71
presomitic mesoderm	6.46e-15	71
presumptive segmental plate	6.46e-15	71
dermomyotome	6.46e-15	71
trunk paraxial mesoderm	6.46e-15	71
dense mesenchyme tissue	7.22e-15	73
multilaminar epithelium	3.47e-14	83
epithelial tube	8.55e-14	117
unilaminar epithelium	1.84e-13	148
splanchnic layer of lateral plate mesoderm	2.81e-13	83
artery	5.81e-13	42
arterial blood vessel	5.81e-13	42
arterial system	5.81e-13	42
skeletal muscle tissue	1.45e-12	62
striated muscle tissue	1.45e-12	62
myotome	1.45e-12	62
vessel	4.98e-12	68
epithelial tube open at both ends	6.38e-12	59
blood vessel	6.38e-12	59
blood vasculature	6.38e-12	59
vascular cord	6.38e-12	59
muscle tissue	1.83e-11	64
musculature	1.83e-11	64
musculature of body	1.83e-11	64
circulatory system	4.80e-11	112
anatomical cluster	5.31e-11	373
cardiovascular system	2.22e-10	109
multi-tissue structure	2.56e-10	342
mesenchyme	9.30e-10	160
entire embryonic mesenchyme	9.30e-10	160
trunk mesenchyme	2.66e-09	122
systemic artery	3.16e-09	33
systemic arterial system	3.16e-09	33
nephron epithelium	2.22e-08	15
renal tubule	2.22e-08	15
nephron tubule	2.22e-08	15
nephron	2.22e-08	15
uriniferous tubule	2.22e-08	15
nephrogenic mesenchyme	2.22e-08	15
trunk	2.90e-08	199
tube	7.49e-08	192
organism subdivision	1.14e-07	264
parenchyma	1.33e-07	15
excretory tube	1.67e-07	16
kidney epithelium	1.67e-07	16
cortex of kidney	4.64e-07	12
renal parenchyma	4.64e-07	12

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)
MA0003.1	2.24383
MA0004.1	0.626788
MA0006.1	0.452993
MA0007.1	0.606704
MA0009.1	1.11255
MA0014.1	3.07977
MA0017.1	0.496101
MA0019.1	0.784036
MA0024.1	1.00439
MA0025.1	1.24931
MA0027.1	2.73598
MA0028.1	3.05902
MA0029.1	1.02437
MA0030.1	1.01252
MA0031.1	0.945567
MA0038.1	0.736268
MA0040.1	1.03042
MA0041.1	0.64667
MA0042.1	0.612397
MA0043.1	1.11288
MA0046.1	1.10134
MA0048.1	0.195817
MA0050.1	0.613347
MA0051.1	0.731787
MA0052.1	1.03442
MA0055.1	0.288856
MA0056.1	0
MA0057.1	0.189508
MA0058.1	0.523638
MA0059.1	0.522232
MA0060.1	1.55172
MA0061.1	0.791444
MA0063.1	0
MA0066.1	0.736721
MA0067.1	1.43651
MA0068.1	0.692739
MA0069.1	1.09737
MA0070.1	1.08584
MA0071.1	0.695094
MA0072.1	1.0812
MA0073.1	0.0140295
MA0074.1	0.730989
MA0076.1	3.37477
MA0077.1	1.07324
MA0078.1	0.836493
MA0081.1	1.2972
MA0083.1	1.12028
MA0084.1	1.62584
MA0087.1	1.07867
MA0088.1	0.132006
MA0089.1	0
MA0090.1	0.556637
MA0091.1	0.629594
MA0092.1	0.588959
MA0093.1	0.456342
MA0095.1	0
MA0098.1	0
MA0100.1	0.750974
MA0101.1	0.459973
MA0103.1	0.442769
MA0105.1	0.175503
MA0106.1	0.779931
MA0107.1	0.378225
MA0108.2	0.94238
MA0109.1	0
MA0111.1	1.40074
MA0113.1	0.797251
MA0114.1	0.372523
MA0115.1	1.35895
MA0116.1	0.382106
MA0117.1	1.1512
MA0119.1	0.504689
MA0122.1	1.17777
MA0124.1	1.31673
MA0125.1	1.23103
MA0130.1	0
MA0131.1	1.99092
MA0132.1	0
MA0133.1	0
MA0135.1	1.14377
MA0136.1	0.743749
MA0139.1	0.277033
MA0140.1	0.692258
MA0141.1	0.520334
MA0142.1	0.912455
MA0143.1	0.797437
MA0144.1	0.356507
MA0145.1	0.143698
MA0146.1	1.35428
MA0147.1	1.00307
MA0148.1	0.653474
MA0149.1	0.681935
MA0062.2	3.94248
MA0035.2	0.691506
MA0039.2	1.92202
MA0138.2	1.95446
MA0002.2	0.30855
MA0137.2	0.47779
MA0104.2	0.858845
MA0047.2	0.767096
MA0112.2	0.136971
MA0065.2	0.146576
MA0150.1	0.550239
MA0151.1	0
MA0152.1	0.69926
MA0153.1	1.21379
MA0154.1	0.172764
MA0155.1	0.813062
MA0156.1	1.20729
MA0157.1	0.883854
MA0158.1	0
MA0159.1	0.386729
MA0160.1	0.669748
MA0161.1	0
MA0162.1	1.23503
MA0163.1	1.05321
MA0164.1	0.810347
MA0080.2	0.456437
MA0018.2	0.781393
MA0099.2	0.699641
MA0079.2	1.03616
MA0102.2	1.66336
MA0258.1	0.345771
MA0259.1	1.80881
MA0442.1	0

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
BCL3#602	2	13.8188411214953	0.00790282333228084	0.0324358628468159
E2F1#1869	4	3.92591137190346	0.00721498454710636	0.0298686289485984
EGR1#1958	4	3.99054327584811	0.006780098300144	0.0287602731964071
ELF1#1997	5	4.25809795880754	0.000714241693977684	0.00572659974492057
ETS1#2113	5	9.72876092220234	1.14685159850452e-05	0.00029213666852735
GABPB1#2553	4	5.65414706894574	0.00177669650209667	0.0109054602399338
HEY1#23462	5	4.04011104310571	0.000928885220517799	0.00673693357955961
IRF1#3659	4	6.10973100285112	0.00131552526476799	0.00880718866199388
MXI1#4601	3	5.97694297725558	0.00865300488936688	0.0329448863563336
MYC#4609	4	4.17782549728752	0.00569196903682344	0.0256721175607533
NFKB1#4790	4	4.39045073935507	0.00470773269252496	0.0221963294963936
NR2C2#7182	2	13.0458443620963	0.0088363641276826	0.0335463843377333
NRF1#4899	3	7.32616766862654	0.00483968981711754	0.022685353656027
POU2F2#5452	3	5.46367443464551	0.0111565009446978	0.0410055886737036
REST#5978	4	7.72002297290242	0.000528636377365057	0.00457189918976724
SIN3A#25942	5	5.40888472681514	0.000215952267165727	0.00247789923429151
SIX5#147912	4	13.6693722843672	5.58844770365977e-05	0.000937292259069411
SP1#6667	4	4.55870510251272	0.0040757356578168	0.0194768133775671
SP2#6668	2	10.4614121975379	0.0135319118334714	0.0477742999112946
TAF1#6872	5	3.34304628574529	0.00239460009087031	0.0135198204611528
TAF7#6879	4	9.14645552393913	0.000272066287241299	0.00290238314332932
TCF12#6938	3	6.38067894131185	0.00718516865325884	0.029825589387031
THAP1#55145	2	12.5476578411405	0.00952843466738653	0.0358880662204617
YY1#7528	4	3.92893659988308	0.00719386626991762	0.0298344200200106
ZEB1#6935	4	13.5107456140351	5.85221769500384e-05	0.00096693523785557

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.