Coexpression cluster:C1357

Full id: C1357_Mesenchymal_Alveolar_Renal_Placental_acantholytic_Tracheal_Bronchial

Phase1 CAGE Peaks

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Hg19::chr12:132628963..132629027,+	p1@NOC4L
Hg19::chr12:53895052..53895143,+	p1@TARBP2
Hg19::chr16:2022036..2022112,+	p1@TBL3
Hg19::chr16:88772866..88772947,+	p1@CTU2
Hg19::chr19:59055814..59055835,+	p1@TRIM28
Hg19::chr19:984313..984357,+	p1@WDR18
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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:0007199	G-protein signaling, coupled to cGMP nucleotide second messenger	0.011538404895764
GO:0019934	cGMP-mediated signaling	0.011538404895764
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.0172999664284364
GO:0030515	snoRNA binding	0.0172999664284364
GO:0005634	nucleus	0.0172999664284364
GO:0043193	positive regulation of gene-specific transcription	0.0172999664284364
GO:0001837	epithelial to mesenchymal transition	0.0172999664284364
GO:0032583	regulation of gene-specific transcription	0.0172999664284364
GO:0005732	small nucleolar ribonucleoprotein complex	0.0192196385985799
GO:0006366	transcription from RNA polymerase II promoter	0.0203185721744452
GO:0048762	mesenchymal cell differentiation	0.0230544017185297
GO:0014031	mesenchymal cell development	0.0230544017185297
GO:0043231	intracellular membrane-bound organelle	0.0295162839166376
GO:0043227	membrane-bound organelle	0.0295162839166376
GO:0003723	RNA binding	0.0295162839166376
GO:0044452	nucleolar part	0.0295162839166376
GO:0003725	double-stranded RNA binding	0.0358917455404646

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
embryonic cell	8.42e-28	250
animal cell	3.59e-25	679
eukaryotic cell	3.59e-25	679
epithelial cell	4.84e-21	253
mesodermal cell	7.82e-17	121
native cell	2.20e-15	722
non-terminally differentiated cell	1.04e-14	106
electrically responsive cell	8.70e-12	61
electrically active cell	8.70e-12	61
contractile cell	3.04e-11	59
somatic cell	3.33e-11	588
muscle cell	1.95e-09	55
muscle precursor cell	7.00e-09	58
myoblast	7.00e-09	58
multi-potent skeletal muscle stem cell	7.00e-09	58
epithelial cell of nephron	1.91e-08	15
meso-epithelial cell	3.39e-08	45
smooth muscle cell	3.78e-08	43
smooth muscle myoblast	3.78e-08	43
endothelial cell	4.11e-08	36
lining cell	5.32e-08	58
barrier cell	5.32e-08	58
blood vessel endothelial cell	7.79e-08	18
embryonic blood vessel endothelial progenitor cell	7.79e-08	18
ectodermal cell	9.40e-08	72
squamous epithelial cell	1.48e-07	63
kidney cortical cell	2.28e-07	12
renal cortical epithelial cell	2.28e-07	12
vascular associated smooth muscle cell	4.42e-07	32
kidney cell	5.47e-07	17
kidney epithelial cell	5.47e-07	17
neurectodermal cell	6.20e-07	59

Uber Anatomy

Ontology term	p-value	n
unilaminar epithelium	1.15e-14	148
epithelial vesicle	1.02e-13	78
epithelial tube	7.07e-13	117
vasculature	7.32e-12	78
vascular system	7.32e-12	78
epithelial tube open at both ends	2.58e-11	59
blood vessel	2.58e-11	59
blood vasculature	2.58e-11	59
vascular cord	2.58e-11	59
vessel	2.82e-11	68
multilaminar epithelium	6.05e-11	83
somite	1.03e-10	71
presomitic mesoderm	1.03e-10	71
presumptive segmental plate	1.03e-10	71
dermomyotome	1.03e-10	71
trunk paraxial mesoderm	1.03e-10	71
splanchnic layer of lateral plate mesoderm	1.98e-10	83
artery	2.18e-10	42
arterial blood vessel	2.18e-10	42
arterial system	2.18e-10	42
mesenchyme	3.59e-10	160
entire embryonic mesenchyme	3.59e-10	160
paraxial mesoderm	3.61e-10	72
presumptive paraxial mesoderm	3.61e-10	72
dense mesenchyme tissue	5.94e-10	73
trunk	2.51e-09	199
trunk mesenchyme	1.07e-08	122
cell layer	1.41e-08	309
nephron epithelium	1.91e-08	15
renal tubule	1.91e-08	15
nephron tubule	1.91e-08	15
nephron	1.91e-08	15
uriniferous tubule	1.91e-08	15
nephrogenic mesenchyme	1.91e-08	15
organism subdivision	2.66e-08	264
epithelium	3.50e-08	306
skeletal muscle tissue	4.42e-08	62
striated muscle tissue	4.42e-08	62
myotome	4.42e-08	62
blood vessel endothelium	7.79e-08	18
endothelium	7.79e-08	18
cardiovascular system endothelium	7.79e-08	18
excretory tube	1.50e-07	16
kidney epithelium	1.50e-07	16
parenchyma	1.60e-07	15
simple squamous epithelium	1.81e-07	22
cortex of kidney	2.28e-07	12
renal parenchyma	2.28e-07	12
muscle tissue	3.12e-07	64
musculature	3.12e-07	64
musculature of body	3.12e-07	64
squamous epithelium	4.59e-07	25
systemic artery	9.96e-07	33
systemic arterial system	9.96e-07	33

Disease

Ontology term	p-value	n
cancer	3.81e-07	235
disease of cellular proliferation	7.76e-07	239

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	4.63763
MA0004.1	0.558729
MA0006.1	1.79433
MA0007.1	1.33289
MA0009.1	1.03681
MA0014.1	0.788761
MA0017.1	0.432438
MA0019.1	0.7124
MA0024.1	0.929647
MA0025.1	1.17262
MA0027.1	2.65688
MA0028.1	0.408079
MA0029.1	0.949428
MA0030.1	0.937696
MA0031.1	0.871496
MA0038.1	0.665566
MA0040.1	0.955415
MA0041.1	0.578072
MA0042.1	0.544748
MA0043.1	2.36158
MA0046.1	1.02569
MA0048.1	0.464411
MA0050.1	0.545671
MA0051.1	0.661179
MA0052.1	0.959373
MA0055.1	0.465994
MA0056.1	0
MA0057.1	0.450439
MA0058.1	0.458909
MA0059.1	0.457555
MA0060.1	0.267412
MA0061.1	0.671725
MA0063.1	0
MA0066.1	0.66601
MA0067.1	1.35893
MA0068.1	0.199491
MA0069.1	1.02175
MA0070.1	1.01032
MA0071.1	0.625297
MA0072.1	1.00572
MA0073.1	0.347876
MA0074.1	0.660398
MA0076.1	0.475586
MA0077.1	0.997832
MA0078.1	0.763954
MA0081.1	0.457725
MA0083.1	1.04447
MA0084.1	1.5477
MA0087.1	1.00322
MA0088.1	1.09824
MA0089.1	0
MA0090.1	0.490736
MA0091.1	0.561458
MA0092.1	0.522012
MA0093.1	0.394379
MA0095.1	0
MA0098.1	0
MA0100.1	0.679972
MA0101.1	0.397846
MA0103.1	0.381434
MA0105.1	0.830067
MA0106.1	1.68738
MA0107.1	0.857383
MA0108.2	0.868347
MA0109.1	0
MA0111.1	0.504913
MA0113.1	0.725375
MA0114.1	0.314898
MA0115.1	1.28169
MA0116.1	0.323925
MA0117.1	1.07516
MA0119.1	0.440684
MA0122.1	1.10154
MA0124.1	1.23968
MA0125.1	1.15445
MA0130.1	0
MA0131.1	0.782708
MA0132.1	0
MA0133.1	0
MA0135.1	1.06778
MA0136.1	0.672893
MA0139.1	1.86787
MA0140.1	0.622527
MA0141.1	0.455728
MA0142.1	0.838805
MA0143.1	0.725558
MA0144.1	0.299851
MA0145.1	1.16614
MA0146.1	2.91645
MA0147.1	1.57246
MA0148.1	0.584698
MA0149.1	0.612449
MA0062.2	0.658749
MA0035.2	0.621793
MA0039.2	0.82735
MA0138.2	0.765223
MA0002.2	0.255126
MA0137.2	0.414885
MA0104.2	2.08061
MA0047.2	0.695777
MA0112.2	0.332548
MA0065.2	0.109623
MA0150.1	0.484557
MA0151.1	0
MA0152.1	0.629368
MA0153.1	1.13732
MA0154.1	0.132326
MA0155.1	0.65596
MA0156.1	0.417278
MA0157.1	0.810597
MA0158.1	0
MA0159.1	0.328286
MA0160.1	0.600559
MA0161.1	0
MA0162.1	2.40092
MA0163.1	0.813808
MA0164.1	0.738243
MA0080.2	0.394469
MA0018.2	5.47519
MA0099.2	0.629739
MA0079.2	0.476723
MA0102.2	1.58513
MA0258.1	0.289793
MA0259.1	2.42942
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
ATF3#467	5	18.7193121050073	1.00898122415384e-06	4.25765616442033e-05
BRCA1#672	5	16.8201922026865	1.71529178571936e-06	6.474281127891e-05
CCNT2#905	6	6.33620157696263	1.54467812014647e-05	0.000362364416419536
CHD2#1106	4	6.89601522274457	0.00111539132013599	0.00766031130950763
CTCFL#140690	4	13.1643162393162	9.07806692187542e-05	0.00132416792074546
E2F1#1869	5	4.08949101239944	0.00174981759776199	0.0107569133022935
E2F4#1874	4	8.44537354352296	0.000511119352377084	0.00443288440814734
E2F6#1876	5	4.18096310974782	0.00157359875958697	0.00997360607188393
EGR1#1958	6	4.98817909481014	6.48943962979974e-05	0.00105453646413047
ELF1#1997	6	4.25809795880754	0.000167722477628883	0.00205162424936553
ETS1#2113	6	9.72876092220234	1.17854759771003e-06	4.80243201549895e-05
FOSL2#2355	3	8.46510030228085	0.00359831563461509	0.0182208235909608
GABPB1#2553	4	4.71178922412145	0.00473005431155596	0.0222854758083905
GTF2F1#2962	4	8.49310725117177	0.000500101731937838	0.0044109555596534
HDAC2#3066	3	6.70781011831313	0.00697394002796266	0.0294867140026878
HEY1#23462	6	4.04011104310571	0.000229896855580751	0.00252978587082478
HMGN3#9324	4	5.45236514890039	0.00272961688233377	0.0149859884126614
IRF1#3659	5	6.36430312796992	0.00020566751420509	0.00243921298161088
JUN#3725	3	6.25641459616817	0.00848634685095487	0.0324084239712914
JUND#3727	5	5.82888661822586	0.000315568248503075	0.00323431131554589
MAX#4149	6	6.45255550900712	1.3848964723355e-05	0.000334421277859532
MEF2A#4205	3	9.37161545482203	0.00268739994710391	0.0147993336712674
MEF2C#4208	3	20.655677246312	0.000268356349406041	0.00286573300364187
MXI1#4601	5	8.30130969063275	5.60234779909565e-05	0.000939321884395169
MYC#4609	6	5.2222818716094	4.92821127172503e-05	0.000853419759588278
NFKB1#4790	6	5.48806342419384	3.65870229532191e-05	0.000706958758595976
NR3C1#2908	4	9.98201555411536	0.000267321918040192	0.00285995019444782
NRF1#4899	3	6.10513972385545	0.00909016207939674	0.0344023567694635
PAX5#5079	6	6.66956553117783	1.13557256338955e-05	0.000289829088337832
POLR2A#5430	6	2.14745317655807	0.0101957067681878	0.038005190204967
RFX5#5993	4	8.0319405514634	0.000620461542838141	0.00510963436937964
SETDB1#9869	2	13.4400087260035	0.00863174120858342	0.0328795105435569
SIN3A#25942	6	5.40888472681514	3.99207083571449e-05	0.000742525175442895
SIX5#147912	5	14.2389294628825	3.91539088341565e-06	0.00012746867471105
SP1#6667	6	5.6983813781409	2.91961319085282e-05	0.000609233730348608
SRF#6722	5	11.4976485518065	1.12681431027194e-05	0.000288016054210697
TAF1#6872	6	3.34304628574529	0.000716247428463562	0.00572816947555755
TAF7#6879	5	9.5275578374366	2.84599232912077e-05	0.000599863961374459
TBP#6908	6	3.70677068709639	0.00038541647290796	0.00377603292814582
TCF7L2#6934	4	7.18011770875823	0.000955329712067973	0.00687430617325803
THAP1#55145	4	20.9127630685675	1.46974095435158e-05	0.000349097738302307
USF1#7391	5	5.3012493976733	0.000500332754985889	0.00441075821709895
YY1#7528	5	4.09264229154488	0.00174336546284953	0.010723561197629
ZEB1#6935	3	8.44421600877193	0.00362384381073359	0.018335866660976
ZNF143#7702	3	6.75043827611395	0.00685025920446858	0.0290354797506288

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.