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

Latest revision as of 10:37, 17 September 2013


Full id: C125_mucinous_alveolar_mesothelioma_Smooth_lung_CD14_Nucleus



Phase1 CAGE Peaks

Hg19::chr10:32872106..32872117,+p@chr10:32872106..32872117
+
Hg19::chr10:34987997..34988013,-p@chr10:34987997..34988013
-
Hg19::chr10:34988014..34988029,-p@chr10:34988014..34988029
-
Hg19::chr10:34988093..34988129,-p@chr10:34988093..34988129
-
Hg19::chr10:44801889..44801898,-p@chr10:44801889..44801898
-
Hg19::chr10:5060201..5060211,-p5@AKR1C2
Hg19::chr10:5136509..5136521,+p4@AKR1C3
Hg19::chr10:70992187..70992196,-p3@ENST00000450995
Hg19::chr10:70992213..70992241,-p1@ENST00000450995
Hg19::chr10:70992318..70992353,+p2@HKDC1
Hg19::chr10:70992359..70992379,+p5@HKDC1
Hg19::chr10:76969764..76969775,+p9@VDAC2
Hg19::chr11:108800179..108800190,+p9@DDX10
Hg19::chr11:76480789..76480811,-p@chr11:76480789..76480811
-
Hg19::chr11:76480816..76480852,-p@chr11:76480816..76480852
-
Hg19::chr11:93465296..93465301,-p1@SNORA1
Hg19::chr12:104671230..104671232,-p@chr12:104671230..104671232
-
Hg19::chr12:104674641..104674651,-p6@ENST00000549807
Hg19::chr12:104982622..104982628,+p13@CHST11
Hg19::chr12:10771068..10771102,-p@chr12:10771068..10771102
-
Hg19::chr12:13025302..13025313,+p@chr12:13025302..13025313
+
Hg19::chr12:15815689..15815698,-p29@EPS8
Hg19::chr12:15815728..15815729,-p37@EPS8
Hg19::chr12:15815732..15815744,-p21@EPS8
Hg19::chr12:1609586..1609598,+p5@LOC100292680
Hg19::chr12:21791511..21791535,-p8@LDHB
Hg19::chr12:21791552..21791567,-p7@LDHB
Hg19::chr12:21791577..21791608,-p6@LDHB
Hg19::chr12:50641120..50641132,+p@chr12:50641120..50641132
+
Hg19::chr12:60015797..60015821,+p@chr12:60015797..60015821
+
Hg19::chr12:61513089..61513090,+p@chr12:61513089..61513090
+
Hg19::chr12:75214368..75214385,+p@chr12:75214368..75214385
+
Hg19::chr12:88693740..88693754,+p@chr12:88693740..88693754
+
Hg19::chr12:88693779..88693791,+p@chr12:88693779..88693791
+
Hg19::chr12:88739033..88739034,+p@chr12:88739033..88739034
+
Hg19::chr12:95571339..95571343,-p@chr12:95571339..95571343
-
Hg19::chr12:98416778..98416782,-p@chr12:98416778..98416782
-
Hg19::chr13:37363331..37363344,-p@chr13:37363331..37363344
-
Hg19::chr13:37363350..37363364,-p@chr13:37363350..37363364
-
Hg19::chr13:73458552..73458595,+p6@PIBF1
Hg19::chr14:29706068..29706072,-p@chr14:29706068..29706072
-
Hg19::chr14:55913197..55913206,-p@chr14:55913197..55913206
-
Hg19::chr14:80683203..80683212,-p@chr14:80683203..80683212
-
Hg19::chr14:80683293..80683297,-p@chr14:80683293..80683297
-
Hg19::chr14:89297734..89297738,+p@chr14:89297734..89297738
+
Hg19::chr17:79881409..79881423,-p8@MAFG
Hg19::chr18:21574704..21574720,-p@chr18:21574704..21574720
-
Hg19::chr18:63273310..63273317,+p@chr18:63273310..63273317
+
Hg19::chr18:71363277..71363286,-p@chr18:71363277..71363286
-
Hg19::chr19:39182748..39182750,+p@chr19:39182748..39182750
+
Hg19::chr1:10480357..10480375,+p@chr1:10480357..10480375
+
Hg19::chr1:10480469..10480472,+p@chr1:10480469..10480472
+
Hg19::chr1:246469336..246469344,-p15@SMYD3
Hg19::chr1:45988542..45988573,-p2@PRDX1
Hg19::chr1:62072099..62072122,+p@chr1:62072099..62072122
+
Hg19::chr1:8933951..8933957,-p@chr1:8933951..8933957
-
Hg19::chr1:94502511..94502519,+p@chr1:94502511..94502519
+
Hg19::chr21:45671797..45671832,-p@chr21:45671797..45671832
-
Hg19::chr2:117844646..117844651,+p@chr2:117844646..117844651
+
Hg19::chr2:117844694..117844699,+p@chr2:117844694..117844699
+
Hg19::chr2:123150473..123150496,+p@chr2:123150473..123150496
+
Hg19::chr2:173417533..173417537,-p@chr2:173417533..173417537
-
Hg19::chr2:19985345..19985386,-p@chr2:19985345..19985386
-
Hg19::chr2:224873590..224873601,+p@chr2:224873590..224873601
+
Hg19::chr2:225434513..225434523,-p29@CUL3
Hg19::chr2:225434538..225434545,-p43@CUL3
Hg19::chr2:234398623..234398628,-p20@USP40
Hg19::chr2:235903637..235903654,+p@chr2:235903637..235903654
+
Hg19::chr2:235903707..235903722,+p@chr2:235903707..235903722
+
Hg19::chr2:29353400..29353413,+p28@CLIP4
Hg19::chr2:60642094..60642124,+p@chr2:60642094..60642124
+
Hg19::chr2:72855783..72855788,+p@chr2:72855783..72855788
+
Hg19::chr2:75466400..75466410,+p@chr2:75466400..75466410
+
Hg19::chr2:75466431..75466447,+p@chr2:75466431..75466447
+
Hg19::chr3:124826952..124826996,-p7@SLC12A8
Hg19::chr3:139199576..139199582,-p5@RBP2
Hg19::chr3:139199589..139199596,-p4@RBP2
Hg19::chr3:139199602..139199615,-p2@RBP2
Hg19::chr3:139199640..139199652,-p3@RBP2
Hg19::chr3:153697368..153697372,+p@chr3:153697368..153697372
+
Hg19::chr3:177364707..177364717,+p@chr3:177364707..177364717
+
Hg19::chr3:27235576..27235597,-p5@NEK10
Hg19::chr3:46204959..46204979,+p3@CCR3
Hg19::chr3:46205262..46205283,+p5@CCR3
Hg19::chr3:54081801..54081827,+p@chr3:54081801..54081827
+
Hg19::chr3:54081908..54081914,+p@chr3:54081908..54081914
+
Hg19::chr3:58631596..58631603,-p@chr3:58631596..58631603
-
Hg19::chr4:102152036..102152041,-p@chr4:102152036..102152041
-
Hg19::chr4:116100188..116100192,-p@chr4:116100188..116100192
-
Hg19::chr4:137426576..137426593,+p@chr4:137426576..137426593
+
Hg19::chr5:10288678..10288702,-p@chr5:10288678..10288702
-
Hg19::chr5:13859633..13859640,+p@chr5:13859633..13859640
+
Hg19::chr5:13860511..13860548,+p1@ENST00000503244
Hg19::chr5:13986147..13986157,+p@chr5:13986147..13986157
+
Hg19::chr5:173822039..173822053,+p@chr5:173822039..173822053
+
Hg19::chr5:179246687..179246707,+p@chr5:179246687..179246707
+
Hg19::chr5:29793807..29793849,+p@chr5:29793807..29793849
+
Hg19::chr5:34526058..34526105,+p@chr5:34526058..34526105
+
Hg19::chr5:34728676..34728679,+p26@RAI14
Hg19::chr5:72141549..72141572,+p@chr5:72141549..72141572
+
Hg19::chr5:72141725..72141727,+p@chr5:72141725..72141727
+
Hg19::chr5:72141969..72142012,+p@chr5:72141969..72142012
+
Hg19::chr5:78439900..78439935,-p@chr5:78439900..78439935
-
Hg19::chr5:84591097..84591104,-p@chr5:84591097..84591104
-
Hg19::chr5:91690025..91690036,+p@chr5:91690025..91690036
+
Hg19::chr6:113330168..113330197,-p@chr6:113330168..113330197
-
Hg19::chr6:125589278..125589288,+p@chr6:125589278..125589288
+
Hg19::chr6:135196569..135196573,-p@chr6:135196569..135196573
-
Hg19::chr6:141742789..141742801,+p@chr6:141742789..141742801
+
Hg19::chr6:141743015..141743025,+p@chr6:141743015..141743025
+
Hg19::chr6:14777773..14777808,-p@chr6:14777773..14777808
-
Hg19::chr6:158461610..158461622,+p@chr6:158461610..158461622
+
Hg19::chr6:161724933..161724947,+p@chr6:161724933..161724947
+
Hg19::chr6:83673328..83673334,-p@chr6:83673328..83673334
-
Hg19::chr7:134212226..134212234,+p5@AKR1B10
Hg19::chr7:39636570..39636595,-p@chr7:39636570..39636595
-
Hg19::chr7:83045406..83045430,+p@chr7:83045406..83045430
+
Hg19::chr8:103549284..103549319,-p@chr8:103549284..103549319
-
Hg19::chr8:117415998..117416010,-p1@ENST00000523110
Hg19::chr8:117416058..117416064,-p2@ENST00000523110
Hg19::chr8:17663434..17663445,-p@chr8:17663434..17663445
-
Hg19::chr8:23918084..23918100,-p@chr8:23918084..23918100
-
Hg19::chr8:32579302..32579316,+p9@NRG1
Hg19::chr8:32579321..32579340,+p10@NRG1
Hg19::chr8:32579341..32579372,+p2@NRG1
Hg19::chr8:62789354..62789363,-p@chr8:62789354..62789363
-
Hg19::chr8:74573966..74573994,-p@chr8:74573966..74573994
-
Hg19::chr9:123163075..123163103,-p17@CDK5RAP2
Hg19::chr9:123163148..123163176,-p18@CDK5RAP2
Hg19::chr9:123165453..123165477,-p6@CDK5RAP2
Hg19::chr9:123165478..123165498,-p2@CDK5RAP2
Hg19::chr9:123165508..123165509,-p20@CDK5RAP2
Hg19::chr9:123165545..123165560,-p3@CDK5RAP2
Hg19::chr9:123165695..123165711,-p11@CDK5RAP2
Hg19::chr9:123165748..123165770,-p5@CDK5RAP2
Hg19::chr9:123165778..123165799,-p8@CDK5RAP2
Hg19::chr9:33233082..33233096,+p@chr9:33233082..33233096
+
Hg19::chr9:98577619..98577666,+p@chr9:98577619..98577666
+
Hg19::chrX:153770412..153770420,+p22@IKBKG
Hg19::chrX:38429930..38429939,+p12@TSPAN7
Hg19::chrX:38429941..38429957,+p6@TSPAN7
Hg19::chrX:38429964..38429975,+p11@TSPAN7


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

p.valueFDRnGenesnPathwayName
3.08879411926494e-050.0097760333874735429Benzo(a)pyrene metabolism (Wikipathways):WP696
2.14511302572539e-050.009776033387473544175metapathway biotransformation (Wikipathways):WP702
0.0001789219686142740.0377525353776118221{POU2F1,21} (Static Module):NA



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:00470263-alpha-hydroxysteroid dehydrogenase (A-specific) activity0.000196426050335292
GO:0047115trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity0.000294517646387335
GO:0016616oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor0.000495130272441399
GO:0016614oxidoreductase activity, acting on CH-OH group of donors0.000495130272441399
GO:0004033aldo-keto reductase activity0.00258215931067551
GO:0016628oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor0.00331866359094554
GO:0006693prostaglandin metabolic process0.00331866359094554
GO:0006692prostanoid metabolic process0.00331866359094554
GO:0005737cytoplasm0.00908720129811135
GO:0016229steroid dehydrogenase activity0.00962304248041086
GO:0044265cellular macromolecule catabolic process0.0158728621380326
GO:0006690icosanoid metabolic process0.0196592456954908
GO:0047017prostaglandin-F synthase activity0.0233314313144762
GO:0009057macromolecule catabolic process0.0243425548611502
GO:0032052bile acid binding0.0384079954882468
GO:0016627oxidoreductase activity, acting on the CH-CH group of donors0.0384079954882468
GO:0008283cell proliferation0.0384079954882468
GO:0007586digestion0.0395363767192471
GO:0044248cellular catabolic process0.0395363767192471
GO:0042808neuronal Cdc2-like kinase binding0.0395363767192471
GO:0030297transmembrane receptor protein tyrosine kinase activator activity0.0395363767192471
GO:0047045testosterone 17-beta-dehydrogenase (NADP+) activity0.0395363767192471
GO:0047756chondroitin 4-sulfotransferase activity0.0395363767192471
GO:0032501multicellular organismal process0.046617552219066
GO:0050327testosterone 17-beta-dehydrogenase activity0.046617552219066
GO:0030971receptor tyrosine kinase binding0.046617552219066



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><br>disease_data<br>

Cell Type
Ontology termp-valuen
mucus secreting cell5.42e-1951
seromucus secreting cell1.55e-982
secretory cell5.81e-0736
Disease
Ontology termp-valuen
mucinous adenocarcinoma5.42e-1951
adenocarcinoma2.15e-0925


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)
MA0003.10
MA0004.10.0238944
MA0006.10.00261083
MA0007.10.0012342
MA0009.10.177378
MA0014.10
MA0017.10.187001
MA0019.10.597195
MA0024.10.0996984
MA0025.11.57956
MA0027.11.29355
MA0028.13.50176e-06
MA0029.10.2713
MA0030.10.772985
MA0031.10.880799
MA0038.10.889775
MA0040.10.826366
MA0041.14.61124
MA0042.10.96564
MA0043.10.706854
MA0046.10.381615
MA0048.10.000153243
MA0050.11.21889
MA0051.10.27914
MA0052.10.526391
MA0055.10.000626705
MA0056.10
MA0057.13.7776e-05
MA0058.10.102715
MA0059.10.16522
MA0060.10.0881102
MA0061.12.37869e-05
MA0063.10
MA0066.10.167227
MA0067.10.543753
MA0068.10.0452035
MA0069.11.96728
MA0070.10.155872
MA0071.10.504699
MA0072.10.152292
MA0073.10
MA0074.10.277522
MA0076.10.000301356
MA0077.10.959721
MA0078.11.07386
MA0081.10.165566
MA0083.10.411493
MA0084.10.826907
MA0087.10.347236
MA0088.18.21577e-06
MA0089.10
MA0090.10.848083
MA0091.10.310552
MA0092.10.130942
MA0093.10.017964
MA0095.10
MA0098.10
MA0100.10.094969
MA0101.10.000927308
MA0103.10.013525
MA0105.11.23535e-06
MA0106.10.0157094
MA0107.10.00257411
MA0108.21.60867
MA0109.10
MA0111.10.107091
MA0113.10.139259
MA0114.10.00215937
MA0115.10.44037
MA0116.17.67773e-05
MA0117.10.462465
MA0119.10.726279
MA0122.10.508336
MA0124.10.387806
MA0125.10.60573
MA0130.10
MA0131.10.00614227
MA0132.10
MA0133.10
MA0135.10.783839
MA0136.10.176929
MA0139.12.45066e-06
MA0140.11.19394
MA0141.10.246437
MA0142.10.145354
MA0143.10.139459
MA0144.10.118068
MA0145.10.000624303
MA0146.17.25372e-12
MA0147.10.00771104
MA0148.11.82974
MA0149.10.0174119
MA0062.29.79981e-08
MA0035.20.492828
MA0039.21.35006e-15
MA0138.20.0283591
MA0002.20.0653252
MA0137.20.319285
MA0104.20.000333805
MA0047.22.46621
MA0112.20.224936
MA0065.20.0181729
MA0150.120.565
MA0151.10
MA0152.10.51866
MA0153.10.96939
MA0154.10.000157373
MA0155.13.07175e-10
MA0156.10.0283473
MA0157.10.675248
MA0158.10
MA0159.10.195558
MA0160.10.602468
MA0161.10
MA0162.10
MA0163.19.84607e-11
MA0164.10.153692
MA0080.20.00777831
MA0018.20.0524077
MA0099.213.8925
MA0079.20
MA0102.20.333632
MA0258.11.19138
MA0259.10.00423441
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
CEBPB#1051462.582202752027765.9558087765293e-105.71183391011886e-08
EP300#2033492.337486933696743.79787354777007e-093.11583751339795e-07
FOS#2353382.407903533366111.9390957584687e-071.05477719749329e-05
FOSL1#8061113.076404062535940.0009971516741837160.0071491400906208
FOSL2#2355161.907628237133710.009977440276803980.037426689356696
JUN#3725332.907911009486612.03666225375693e-081.45093430504856e-06
JUNB#3726132.802381863223060.0008245495891319770.00627524116733619
JUND#3727542.659942625781942.55805097394752e-123.44722949249168e-10
MAFF#23764155.948805263022384.40808559252356e-082.88999404392698e-06
MAFK#7975366.870608401139983.18013373121331e-208.18054154566962e-18
NFE2#4778179.242763599138696.73642927467144e-128.59030448128707e-10
NR3C1#2908404.217753051034663.38099307939824e-156.04636192156288e-13
STAT3#6774352.592825879580271.17357416348617e-076.77165260001836e-06
TFAP2C#7022221.674669221245950.01145256104528040.04189911454822



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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