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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0,

Latest revision as of 10:46, 17 September 2013


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

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

GO IDGO nameFDR corrected p-value
GO:0030036actin cytoskeleton organization and biogenesis0.0201157464163886
GO:0030029actin filament-based process0.0201157464163886
GO:0001666response to hypoxia0.0201157464163886
GO:0014065phosphoinositide 3-kinase cascade0.0201157464163886
GO:0048715negative regulation of oligodendrocyte differentiation0.0201157464163886
GO:0021897forebrain astrocyte development0.0201157464163886
GO:0021896forebrain astrocyte differentiation0.0201157464163886
GO:0048745smooth muscle development0.0201157464163886
GO:0048485sympathetic nervous system development0.0201157464163886
GO:0048713regulation of oligodendrocyte differentiation0.0201157464163886
GO:0022011myelination in the peripheral nervous system0.0201157464163886
GO:0048854brain morphogenesis0.0201157464163886
GO:0032292ensheathment of axons in the peripheral nervous system0.0201157464163886
GO:0048853forebrain morphogenesis0.0201157464163886
GO:0043409negative regulation of MAPKKK cascade0.0201157464163886
GO:0048844artery morphogenesis0.0201157464163886
GO:0014014negative regulation of gliogenesis0.0201157464163886
GO:0045686negative regulation of glial cell differentiation0.0201157464163886
GO:0043535regulation of blood vessel endothelial cell migration0.0201157464163886
GO:0008334histone mRNA metabolic process0.0201157464163886
GO:0019834phospholipase A2 inhibitor activity0.0201157464163886
GO:0008475procollagen-lysine 5-dioxygenase activity0.0201157464163886
GO:0007406negative regulation of neuroblast proliferation0.0201157464163886
GO:0014044Schwann cell development0.0201157464163886
GO:0048483autonomic nervous system development0.0201157464163886
GO:0014037Schwann cell differentiation0.0201157464163886
GO:0021987cerebral cortex development0.0232400732033849
GO:0050890cognition0.0232400732033849
GO:0043534blood vessel endothelial cell migration0.0232400732033849
GO:0014002astrocyte development0.0232400732033849
GO:0008092cytoskeletal protein binding0.0264037330716217
GO:0008486diphosphoinositol-polyphosphate diphosphatase activity0.0264037330716217
GO:0030325adrenal gland development0.0264037330716217
GO:0045124regulation of bone resorption0.0307290422170373
GO:0021543pallium development0.0307290422170373
GO:0045685regulation of glial cell differentiation0.0307290422170373
GO:0014013regulation of gliogenesis0.0307290422170373
GO:0032320positive regulation of Ras GTPase activity0.0307290422170373
GO:0008542visual learning0.0307290422170373
GO:0007010cytoskeleton organization and biogenesis0.0307290422170373
GO:0048708astrocyte differentiation0.0339818460437372
GO:0043525positive regulation of neuron apoptosis0.0373116614685102
GO:0007632visual behavior0.0375400593471159
GO:0001889liver development0.0375400593471159
GO:0030199collagen fibril organization0.0375400593471159
GO:0021510spinal cord development0.0375400593471159
GO:0030867rough endoplasmic reticulum membrane0.0375400593471159
GO:0021537telencephalon development0.0375400593471159
GO:0042308negative regulation of protein import into nucleus0.0375400593471159
GO:0042992negative regulation of transcription factor import into nucleus0.0375400593471159
GO:0048709oligodendrocyte differentiation0.0375400593471159
GO:0050768negative regulation of neurogenesis0.0376951644035807
GO:0001937negative regulation of endothelial cell proliferation0.0376951644035807
GO:0046823negative regulation of nucleocytoplasmic transport0.0376951644035807
GO:0043542endothelial cell migration0.0376951644035807
GO:0048593camera-type eye morphogenesis0.0376951644035807
GO:0045453bone resorption0.0376951644035807
GO:0051224negative regulation of protein transport0.0376951644035807
GO:0021782glial cell development0.0376951644035807
GO:0001952regulation of cell-matrix adhesion0.0376951644035807
GO:0043408regulation of MAPKKK cascade0.0427637789090141
GO:0007405neuroblast proliferation0.0454643875921512
GO:0001936regulation of endothelial cell proliferation0.0454643875921512
GO:0005791rough endoplasmic reticulum0.0454643875921512
GO:0007612learning0.0454643875921512
GO:0004859phospholipase inhibitor activity0.0458540850453024
GO:0016998cell wall catabolic process0.0458540850453024
GO:0048871multicellular organismal homeostasis0.0458540850453024
GO:0001935endothelial cell proliferation0.0458540850453024
GO:0055102lipase inhibitor activity0.0458540850453024
GO:0030336negative regulation of cell migration0.0458540850453024
GO:0001894tissue homeostasis0.0458540850453024
GO:0010382cell wall metabolic process0.0469532635158058
GO:0007047cell wall organization and biogenesis0.0469532635158058
GO:0042990regulation of transcription factor import into nucleus0.0469930026170049
GO:0042991transcription factor import into nucleus0.0469930026170049
GO:0006400tRNA modification0.0469930026170049
GO:0042306regulation of protein import into nucleus0.0469930026170049
GO:0045229external encapsulating structure organization and biogenesis0.0469930026170049
GO:0031418L-ascorbic acid binding0.0469930026170049
GO:0033157regulation of intracellular protein transport0.0469930026170049
GO:0051271negative regulation of cell motility0.0469930026170049
GO:0000049tRNA binding0.0469930026170049
GO:0007422peripheral nervous system development0.0469930026170049
GO:0043407negative regulation of MAP kinase activity0.0469930026170049
GO:0040013negative regulation of locomotion0.0469930026170049
GO:0046850regulation of bone remodeling0.0469930026170049
GO:0001656metanephros development0.0469930026170049
GO:0001649osteoblast differentiation0.0469930026170049
GO:0043523regulation of neuron apoptosis0.0469930026170049
GO:0032386regulation of intracellular transport0.0469930026170049
GO:0048592eye morphogenesis0.0469930026170049
GO:0051349positive regulation of lyase activity0.0469930026170049
GO:0042552myelination0.0469930026170049
GO:0045762positive regulation of adenylate cyclase activity0.0469930026170049
GO:0031281positive regulation of cyclase activity0.0469930026170049
GO:0006928cell motility0.0485635400987374
GO:0051674localization of cell0.0485635400987374
GO:0051223regulation of protein transport0.0485635400987374
GO:0006383transcription from RNA polymerase III promoter0.0485635400987374
GO:0046822regulation of nucleocytoplasmic transport0.0493015702913813
GO:0010001glial cell differentiation0.0493015702913813



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>

Cell Type
Ontology termp-valuen
cortical cell of adrenal gland2.74e-502
steroid hormone secreting cell4.27e-343
mesothelial cell5.37e-2219
glandular epithelial cell2.19e-129
endocrine cell2.19e-129
lining cell4.33e-0858
barrier cell4.33e-0858
squamous epithelial cell1.52e-0763
Uber Anatomy
Ontology termp-valuen
adrenal gland4.27e-343
adrenal cortex4.27e-343
adrenal/interrenal gland4.27e-343
cortex5.55e-0815
Disease
Ontology termp-valuen
endocrine gland cancer7.67e-186


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

Novel motifs



JASPAR motifs

Motifs-log10(p-value)
MA0003.12.89298e-16
MA0004.10.0772261
MA0006.10.00185537
MA0007.10.130703
MA0009.10.282037
MA0014.19.99525e-14
MA0017.10.479859
MA0019.10.125327
MA0024.10.0472324
MA0025.10.443345
MA0027.11.4058
MA0028.10.00270931
MA0029.11.63295
MA0030.10.185596
MA0031.10.31224
MA0038.10.547352
MA0040.10.444381
MA0041.10.0934058
MA0042.10.137712
MA0043.10.282382
MA0046.10.570295
MA0048.10.00146068
MA0050.11.33472
MA0051.11.07441
MA0052.10.204999
MA0055.10.00013321
MA0056.10
MA0057.15.37488e-05
MA0058.10.0221921
MA0059.10.0517527
MA0060.10.000720001
MA0061.10.158707
MA0063.10
MA0066.10.191627
MA0067.10.2546
MA0068.10.139863
MA0069.10.266146
MA0070.11.38269
MA0071.10.0615472
MA0072.10.909401
MA0073.12.65431e-12
MA0074.10.0839539
MA0076.10.00223929
MA0077.10.241788
MA0078.10.581654
MA0081.10.286731
MA0083.11.51125
MA0084.10.390659
MA0087.10.528631
MA0088.10.00129186
MA0089.10
MA0090.11.85066
MA0091.10.0088069
MA0092.10.110258
MA0093.10.0431055
MA0095.10
MA0098.10
MA0100.10.210951
MA0101.10.149876
MA0103.10.194522
MA0105.10.0151446
MA0106.10.253333
MA0107.10.523196
MA0108.20.563137
MA0109.10
MA0111.10.282469
MA0113.10.738384
MA0114.10.266136
MA0115.10.205538
MA0116.10.00413547
MA0117.10.098373
MA0119.10.242823
MA0122.10.355054
MA0124.13.88176
MA0125.10.420019
MA0130.10
MA0131.10.0167544
MA0132.10
MA0133.10
MA0135.10.0952705
MA0136.10.201028
MA0139.15.03943e-06
MA0140.10.892252
MA0141.10.00152685
MA0142.10.266706
MA0143.10.482216
MA0144.10.53933
MA0145.10.00528615
MA0146.17.56739e-10
MA0147.10.000333388
MA0148.10.984952
MA0149.10.00269981
MA0062.27.4273e-06
MA0035.24.74588
MA0039.24.5583e-11
MA0138.20.0144107
MA0002.20.507098
MA0137.20.563569
MA0104.20.000699262
MA0047.21.24792
MA0112.22.65962e-05
MA0065.20.159306
MA0150.10.139306
MA0151.10
MA0152.10.444126
MA0153.10.126593
MA0154.10.078705
MA0155.10.00747194
MA0156.10.29044
MA0157.10.713023
MA0158.10
MA0159.10.146845
MA0160.10.220576
MA0161.10
MA0162.11.79317e-13
MA0163.17.22632e-07
MA0164.11.88706
MA0080.20.0832983
MA0018.20.0437859
MA0099.20.445135
MA0079.20
MA0102.20.419911
MA0258.10.0762043
MA0259.15.81208e-06
MA0442.10



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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
GATA2#2624171.98774164651760.004919180265394170.0229908828308199
NR3C1#2908152.060507797867850.006001359466156240.0269048755703079



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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