Coexpression cluster:C161

Full id: C161_mesothelioma_Mesothelial_acute_mesenchymal_extraskeletal_renal_placenta

Phase1 CAGE Peaks

Hg19::chr11:117150581..117150628,+	p@chr11:117150581..117150628 +
Hg19::chr11:117150669..117150717,+	p@chr11:117150669..117150717 +
Hg19::chr11:117152141..117152162,+	p10@RNF214
Hg19::chr11:117152220..117152232,+	p11@RNF214
Hg19::chr11:117152916..117152936,+	p9@RNF214
Hg19::chr11:22707203..22707221,+	p@chr11:22707203..22707221 +
Hg19::chr11:65629516..65629528,-	p29@CFL1
Hg19::chr11:65629672..65629698,+	p@chr11:65629672..65629698 +
Hg19::chr11:7506790..7506795,+	p9@OLFML1
Hg19::chr11:79794715..79794718,-	p@chr11:79794715..79794718 -
Hg19::chr11:90224851..90224891,+	p1@AB593165
Hg19::chr12:120502465..120502470,+	p12@CCDC64
Hg19::chr12:80838009..80838023,+	p3@PTPRQ
Hg19::chr12:80838029..80838066,+	p1@PTPRQ
Hg19::chr12:80838067..80838088,+	p2@PTPRQ
Hg19::chr12:80838145..80838152,+	p9@PTPRQ
Hg19::chr12:80952271..80952274,+	p@chr12:80952271..80952274 +
Hg19::chr14:105952794..105952805,+	p18@CRIP1
Hg19::chr14:78718132..78718157,+	p@chr14:78718132..78718157 +
Hg19::chr15:83954702..83954728,-	p@chr15:83954702..83954728 -
Hg19::chr16:33408291..33408306,+	p@chr16:33408291..33408306 +
Hg19::chr16:33408523..33408542,+	p@chr16:33408523..33408542 +
Hg19::chr17:29486054..29486065,+	p12@NF1
Hg19::chr17:31107844..31107872,-	p5@MYO1D
Hg19::chr17:4623333..4623376,+	p@chr17:4623333..4623376 +
Hg19::chr17:4846101..4846106,+	p@chr17:4846101..4846106 +
Hg19::chr17:4847813..4847819,+	p@chr17:4847813..4847819 +
Hg19::chr17:55522578..55522616,+	p@chr17:55522578..55522616 +
Hg19::chr17:8639180..8639188,-	p@chr17:8639180..8639188 -
Hg19::chr18:39541931..39541944,+	p@chr18:39541931..39541944 +
Hg19::chr18:47407103..47407112,-	p@chr18:47407103..47407112 -
Hg19::chr18:60661179..60661191,+	p@chr18:60661179..60661191 +
Hg19::chr19:16199781..16199806,+	p@chr19:16199781..16199806 +
Hg19::chr19:38902076..38902104,-	p@chr19:38902076..38902104 -
Hg19::chr1:168165301..168165329,+	p@chr1:168165301..168165329 +
Hg19::chr1:168165589..168165617,+	p@chr1:168165589..168165617 +
Hg19::chr1:197099062..197099073,-	p@chr1:197099062..197099073 -
Hg19::chr1:197099076..197099083,-	p@chr1:197099076..197099083 -
Hg19::chr1:197099091..197099102,-	p@chr1:197099091..197099102 -
Hg19::chr1:39851487..39851521,+	p@chr1:39851487..39851521 +
Hg19::chr20:36713497..36713503,+	p19@RPRD1B
Hg19::chr22:43355701..43355741,-	p14@PACSIN2
Hg19::chr2:123706107..123706109,-	p@chr2:123706107..123706109 -
Hg19::chr2:135893438..135893485,+	p@chr2:135893438..135893485 +
Hg19::chr2:140624829..140624870,+	p@chr2:140624829..140624870 +
Hg19::chr2:159375045..159375057,+	p@chr2:159375045..159375057 +
Hg19::chr2:165630270..165630300,-	p10@COBLL1
Hg19::chr2:165630301..165630310,-	p39@COBLL1
Hg19::chr2:165630313..165630339,-	p11@COBLL1
Hg19::chr2:165650899..165650926,-	p@chr2:165650899..165650926 -
Hg19::chr2:170115546..170115580,-	p@chr2:170115546..170115580 -
Hg19::chr2:170664937..170664947,+	p13@SSB
Hg19::chr2:204266094..204266122,+	p@chr2:204266094..204266122 +
Hg19::chr3:111812180..111812186,+	p@chr3:111812180..111812186 +
Hg19::chr3:120188917..120188936,+	p@chr3:120188917..120188936 +
Hg19::chr3:145881495..145881517,-	p11@PLOD2
Hg19::chr3:145959753..145959785,-	p@chr3:145959753..145959785 -
Hg19::chr3:165535017..165535020,-	p@chr3:165535017..165535020 -
Hg19::chr3:165535021..165535029,-	p@chr3:165535021..165535029 -
Hg19::chr3:191074565..191074573,+	p@chr3:191074565..191074573 +
Hg19::chr3:191074587..191074598,+	p@chr3:191074587..191074598 +
Hg19::chr3:191074642..191074664,+	p@chr3:191074642..191074664 +
Hg19::chr3:191074675..191074688,+	p@chr3:191074675..191074688 +
Hg19::chr3:191074968..191074971,+	p@chr3:191074968..191074971 +
Hg19::chr3:191074978..191074992,+	p@chr3:191074978..191074992 +
Hg19::chr3:191075002..191075014,+	p@chr3:191075002..191075014 +
Hg19::chr3:191075031..191075040,+	p@chr3:191075031..191075040 +
Hg19::chr3:191075256..191075261,+	p@chr3:191075256..191075261 +
Hg19::chr3:37986042..37986090,-	p@chr3:37986042..37986090 -
Hg19::chr4:106656882..106656914,+	p@chr4:106656882..106656914 +
Hg19::chr4:44869447..44869474,+	p@chr4:44869447..44869474 +
Hg19::chr4:71108300..71108323,+	p1@CSN3
Hg19::chr4:73435069..73435082,-	p@chr4:73435069..73435082 -
Hg19::chr4:79475019..79475042,+	p6@ANXA3
Hg19::chr4:79475120..79475133,+	p5@ANXA3
Hg19::chr5:107631924..107631930,-	p@chr5:107631924..107631930 -
Hg19::chr5:107631933..107631940,-	p@chr5:107631933..107631940 -
Hg19::chr5:107631942..107631951,-	p@chr5:107631942..107631951 -
Hg19::chr5:13428853..13428866,+	p@chr5:13428853..13428866 +
Hg19::chr5:145427166..145427178,+	p@chr5:145427166..145427178 +
Hg19::chr5:179894479..179894489,+	p@chr5:179894479..179894489 +
Hg19::chr5:80434077..80434082,+	p@chr5:80434077..80434082 +
Hg19::chr6:126135900..126135924,+	p22@NCOA7
Hg19::chr6:168251020..168251028,+	p@chr6:168251020..168251028 +
Hg19::chr6:168251039..168251042,+	p@chr6:168251039..168251042 +
Hg19::chr6:19154273..19154282,-	p@chr6:19154273..19154282 -
Hg19::chr6:19154283..19154295,-	p@chr6:19154283..19154295 -
Hg19::chr6:30449373..30449383,-	p@chr6:30449373..30449383 -
Hg19::chr6:45917165..45917177,-	p@chr6:45917165..45917177 -
Hg19::chr6:45917192..45917193,-	p@chr6:45917192..45917193 -
Hg19::chr6:53658203..53658215,-	p@chr6:53658203..53658215 -
Hg19::chr6:64999168..64999210,+	p@chr6:64999168..64999210 +
Hg19::chr7:152166747..152166750,+	p@chr7:152166747..152166750 +
Hg19::chr7:152166833..152166847,+	p@chr7:152166833..152166847 +
Hg19::chr7:33397558..33397583,+	p@chr7:33397558..33397583 +
Hg19::chr7:33397752..33397755,+	p@chr7:33397752..33397755 +
Hg19::chr7:80365907..80365910,-	p@chr7:80365907..80365910 -
Hg19::chr7:80365917..80365926,-	p@chr7:80365917..80365926 -
Hg19::chr7:80365936..80365942,-	p@chr7:80365936..80365942 -
Hg19::chr8:37728955..37729014,-	p@chr8:37728955..37729014 -
Hg19::chr9:123128390..123128421,-	p@chr9:123128390..123128421 -
Hg19::chr9:3330877..3330914,-	p@chr9:3330877..3330914 -
Hg19::chr9:88939319..88939326,-	p25@ZCCHC6
Hg19::chrX:117553200..117553220,+	p@chrX:117553200..117553220 +
Hg19::chrX:140048723..140048740,+	p@chrX:140048723..140048740 +
Hg19::chrX:32584018..32584035,-	p@chrX:32584018..32584035 -
Hg19::chrX:32584039..32584049,-	p@chrX:32584039..32584049 -
Hg19::chrX:64898352..64898387,+	p10@MSN
Hg19::chrY:8692267..8692276,-	p@chrY:8692267..8692276 -

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:0030036	actin cytoskeleton organization and biogenesis	0.0201157464163886
GO:0030029	actin filament-based process	0.0201157464163886
GO:0001666	response to hypoxia	0.0201157464163886
GO:0014065	phosphoinositide 3-kinase cascade	0.0201157464163886
GO:0048715	negative regulation of oligodendrocyte differentiation	0.0201157464163886
GO:0021897	forebrain astrocyte development	0.0201157464163886
GO:0021896	forebrain astrocyte differentiation	0.0201157464163886
GO:0048745	smooth muscle development	0.0201157464163886
GO:0048485	sympathetic nervous system development	0.0201157464163886
GO:0048713	regulation of oligodendrocyte differentiation	0.0201157464163886
GO:0022011	myelination in the peripheral nervous system	0.0201157464163886
GO:0048854	brain morphogenesis	0.0201157464163886
GO:0032292	ensheathment of axons in the peripheral nervous system	0.0201157464163886
GO:0048853	forebrain morphogenesis	0.0201157464163886
GO:0043409	negative regulation of MAPKKK cascade	0.0201157464163886
GO:0048844	artery morphogenesis	0.0201157464163886
GO:0014014	negative regulation of gliogenesis	0.0201157464163886
GO:0045686	negative regulation of glial cell differentiation	0.0201157464163886
GO:0043535	regulation of blood vessel endothelial cell migration	0.0201157464163886
GO:0008334	histone mRNA metabolic process	0.0201157464163886
GO:0019834	phospholipase A2 inhibitor activity	0.0201157464163886
GO:0008475	procollagen-lysine 5-dioxygenase activity	0.0201157464163886
GO:0007406	negative regulation of neuroblast proliferation	0.0201157464163886
GO:0014044	Schwann cell development	0.0201157464163886
GO:0048483	autonomic nervous system development	0.0201157464163886
GO:0014037	Schwann cell differentiation	0.0201157464163886
GO:0021987	cerebral cortex development	0.0232400732033849
GO:0050890	cognition	0.0232400732033849
GO:0043534	blood vessel endothelial cell migration	0.0232400732033849
GO:0014002	astrocyte development	0.0232400732033849
GO:0008092	cytoskeletal protein binding	0.0264037330716217
GO:0008486	diphosphoinositol-polyphosphate diphosphatase activity	0.0264037330716217
GO:0030325	adrenal gland development	0.0264037330716217
GO:0045124	regulation of bone resorption	0.0307290422170373
GO:0021543	pallium development	0.0307290422170373
GO:0045685	regulation of glial cell differentiation	0.0307290422170373
GO:0014013	regulation of gliogenesis	0.0307290422170373
GO:0032320	positive regulation of Ras GTPase activity	0.0307290422170373
GO:0008542	visual learning	0.0307290422170373
GO:0007010	cytoskeleton organization and biogenesis	0.0307290422170373
GO:0048708	astrocyte differentiation	0.0339818460437372
GO:0043525	positive regulation of neuron apoptosis	0.0373116614685102
GO:0007632	visual behavior	0.0375400593471159
GO:0001889	liver development	0.0375400593471159
GO:0030199	collagen fibril organization	0.0375400593471159
GO:0021510	spinal cord development	0.0375400593471159
GO:0030867	rough endoplasmic reticulum membrane	0.0375400593471159
GO:0021537	telencephalon development	0.0375400593471159
GO:0042308	negative regulation of protein import into nucleus	0.0375400593471159
GO:0042992	negative regulation of transcription factor import into nucleus	0.0375400593471159
GO:0048709	oligodendrocyte differentiation	0.0375400593471159
GO:0050768	negative regulation of neurogenesis	0.0376951644035807
GO:0001937	negative regulation of endothelial cell proliferation	0.0376951644035807
GO:0046823	negative regulation of nucleocytoplasmic transport	0.0376951644035807
GO:0043542	endothelial cell migration	0.0376951644035807
GO:0048593	camera-type eye morphogenesis	0.0376951644035807
GO:0045453	bone resorption	0.0376951644035807
GO:0051224	negative regulation of protein transport	0.0376951644035807
GO:0021782	glial cell development	0.0376951644035807
GO:0001952	regulation of cell-matrix adhesion	0.0376951644035807
GO:0043408	regulation of MAPKKK cascade	0.0427637789090141
GO:0007405	neuroblast proliferation	0.0454643875921512
GO:0001936	regulation of endothelial cell proliferation	0.0454643875921512
GO:0005791	rough endoplasmic reticulum	0.0454643875921512
GO:0007612	learning	0.0454643875921512
GO:0004859	phospholipase inhibitor activity	0.0458540850453024
GO:0016998	cell wall catabolic process	0.0458540850453024
GO:0048871	multicellular organismal homeostasis	0.0458540850453024
GO:0001935	endothelial cell proliferation	0.0458540850453024
GO:0055102	lipase inhibitor activity	0.0458540850453024
GO:0030336	negative regulation of cell migration	0.0458540850453024
GO:0001894	tissue homeostasis	0.0458540850453024
GO:0010382	cell wall metabolic process	0.0469532635158058
GO:0007047	cell wall organization and biogenesis	0.0469532635158058
GO:0042990	regulation of transcription factor import into nucleus	0.0469930026170049
GO:0042991	transcription factor import into nucleus	0.0469930026170049
GO:0006400	tRNA modification	0.0469930026170049
GO:0042306	regulation of protein import into nucleus	0.0469930026170049
GO:0045229	external encapsulating structure organization and biogenesis	0.0469930026170049
GO:0031418	L-ascorbic acid binding	0.0469930026170049
GO:0033157	regulation of intracellular protein transport	0.0469930026170049
GO:0051271	negative regulation of cell motility	0.0469930026170049
GO:0000049	tRNA binding	0.0469930026170049
GO:0007422	peripheral nervous system development	0.0469930026170049
GO:0043407	negative regulation of MAP kinase activity	0.0469930026170049
GO:0040013	negative regulation of locomotion	0.0469930026170049
GO:0046850	regulation of bone remodeling	0.0469930026170049
GO:0001656	metanephros development	0.0469930026170049
GO:0001649	osteoblast differentiation	0.0469930026170049
GO:0043523	regulation of neuron apoptosis	0.0469930026170049
GO:0032386	regulation of intracellular transport	0.0469930026170049
GO:0048592	eye morphogenesis	0.0469930026170049
GO:0051349	positive regulation of lyase activity	0.0469930026170049
GO:0042552	myelination	0.0469930026170049
GO:0045762	positive regulation of adenylate cyclase activity	0.0469930026170049
GO:0031281	positive regulation of cyclase activity	0.0469930026170049
GO:0006928	cell motility	0.0485635400987374
GO:0051674	localization of cell	0.0485635400987374
GO:0051223	regulation of protein transport	0.0485635400987374
GO:0006383	transcription from RNA polymerase III promoter	0.0485635400987374
GO:0046822	regulation of nucleocytoplasmic transport	0.0493015702913813
GO:0010001	glial cell differentiation	0.0493015702913813

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
cortical cell of adrenal gland	2.74e-50	2
steroid hormone secreting cell	4.27e-34	3
mesothelial cell	5.37e-22	19
glandular epithelial cell	2.19e-12	9
endocrine cell	2.19e-12	9
lining cell	4.33e-08	58
barrier cell	4.33e-08	58
squamous epithelial cell	1.52e-07	63

Uber Anatomy

Ontology term	p-value	n
adrenal gland	4.27e-34	3
adrenal cortex	4.27e-34	3
adrenal/interrenal gland	4.27e-34	3
cortex	5.55e-08	15

Disease

Ontology term	p-value	n
endocrine gland cancer	7.67e-18	6

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	2.89298e-16
MA0004.1	0.0772261
MA0006.1	0.00185537
MA0007.1	0.130703
MA0009.1	0.282037
MA0014.1	9.99525e-14
MA0017.1	0.479859
MA0019.1	0.125327
MA0024.1	0.0472324
MA0025.1	0.443345
MA0027.1	1.4058
MA0028.1	0.00270931
MA0029.1	1.63295
MA0030.1	0.185596
MA0031.1	0.31224
MA0038.1	0.547352
MA0040.1	0.444381
MA0041.1	0.0934058
MA0042.1	0.137712
MA0043.1	0.282382
MA0046.1	0.570295
MA0048.1	0.00146068
MA0050.1	1.33472
MA0051.1	1.07441
MA0052.1	0.204999
MA0055.1	0.00013321
MA0056.1	0
MA0057.1	5.37488e-05
MA0058.1	0.0221921
MA0059.1	0.0517527
MA0060.1	0.000720001
MA0061.1	0.158707
MA0063.1	0
MA0066.1	0.191627
MA0067.1	0.2546
MA0068.1	0.139863
MA0069.1	0.266146
MA0070.1	1.38269
MA0071.1	0.0615472
MA0072.1	0.909401
MA0073.1	2.65431e-12
MA0074.1	0.0839539
MA0076.1	0.00223929
MA0077.1	0.241788
MA0078.1	0.581654
MA0081.1	0.286731
MA0083.1	1.51125
MA0084.1	0.390659
MA0087.1	0.528631
MA0088.1	0.00129186
MA0089.1	0
MA0090.1	1.85066
MA0091.1	0.0088069
MA0092.1	0.110258
MA0093.1	0.0431055
MA0095.1	0
MA0098.1	0
MA0100.1	0.210951
MA0101.1	0.149876
MA0103.1	0.194522
MA0105.1	0.0151446
MA0106.1	0.253333
MA0107.1	0.523196
MA0108.2	0.563137
MA0109.1	0
MA0111.1	0.282469
MA0113.1	0.738384
MA0114.1	0.266136
MA0115.1	0.205538
MA0116.1	0.00413547
MA0117.1	0.098373
MA0119.1	0.242823
MA0122.1	0.355054
MA0124.1	3.88176
MA0125.1	0.420019
MA0130.1	0
MA0131.1	0.0167544
MA0132.1	0
MA0133.1	0
MA0135.1	0.0952705
MA0136.1	0.201028
MA0139.1	5.03943e-06
MA0140.1	0.892252
MA0141.1	0.00152685
MA0142.1	0.266706
MA0143.1	0.482216
MA0144.1	0.53933
MA0145.1	0.00528615
MA0146.1	7.56739e-10
MA0147.1	0.000333388
MA0148.1	0.984952
MA0149.1	0.00269981
MA0062.2	7.4273e-06
MA0035.2	4.74588
MA0039.2	4.5583e-11
MA0138.2	0.0144107
MA0002.2	0.507098
MA0137.2	0.563569
MA0104.2	0.000699262
MA0047.2	1.24792
MA0112.2	2.65962e-05
MA0065.2	0.159306
MA0150.1	0.139306
MA0151.1	0
MA0152.1	0.444126
MA0153.1	0.126593
MA0154.1	0.078705
MA0155.1	0.00747194
MA0156.1	0.29044
MA0157.1	0.713023
MA0158.1	0
MA0159.1	0.146845
MA0160.1	0.220576
MA0161.1	0
MA0162.1	1.79317e-13
MA0163.1	7.22632e-07
MA0164.1	1.88706
MA0080.2	0.0832983
MA0018.2	0.0437859
MA0099.2	0.445135
MA0079.2	0
MA0102.2	0.419911
MA0258.1	0.0762043
MA0259.1	5.81208e-06
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
GATA2#2624	17	1.9877416465176	0.00491918026539417	0.0229908828308199
NR3C1#2908	15	2.06050779786785	0.00600135946615624	0.0269048755703079

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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