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{{Coexpression_clusters
{
|full_id=C117_serous_clear_kidney_neuroectodermal_mesothelioma_endometrial_Intestinal
 

Latest revision as of 10:35, 17 September 2013


Full id: C117_serous_clear_kidney_neuroectodermal_mesothelioma_endometrial_Intestinal



Phase1 CAGE Peaks

Hg19::chr10:3305882..3305893,+p@chr10:3305882..3305893
+
Hg19::chr10:85857839..85857840,-p@chr10:85857839..85857840
-
Hg19::chr10:85931768..85931785,-p4@ENST00000514797
p4@uc001kct.2
Hg19::chr10:85931846..85931867,-p1@ENST00000514797
p1@uc001kct.2
Hg19::chr10:96731879..96731924,+p@chr10:96731879..96731924
+
Hg19::chr11:11833036..11833048,-p@chr11:11833036..11833048
-
Hg19::chr11:89223721..89223728,-p@chr11:89223721..89223728
-
Hg19::chr12:123070114..123070123,+p@chr12:123070114..123070123
+
Hg19::chr12:132680939..132680977,+p@chr12:132680939..132680977
+
Hg19::chr12:132681008..132681011,+p@chr12:132681008..132681011
+
Hg19::chr12:132681018..132681026,+p@chr12:132681018..132681026
+
Hg19::chr12:132681039..132681046,+p@chr12:132681039..132681046
+
Hg19::chr12:132681059..132681070,+p@chr12:132681059..132681070
+
Hg19::chr12:31652588..31652610,-p@chr12:31652588..31652610
-
Hg19::chr12:39104065..39104071,-p@chr12:39104065..39104071
-
Hg19::chr13:23467567..23467577,+p@chr13:23467567..23467577
+
Hg19::chr13:23479449..23479452,+p@chr13:23479449..23479452
+
Hg19::chr13:23486051..23486062,+p@chr13:23486051..23486062
+
Hg19::chr14:64405176..64405183,+p@chr14:64405176..64405183
+
Hg19::chr15:75397998..75398004,-p@chr15:75397998..75398004
-
Hg19::chr16:2106134..2106163,+p18@TSC2
Hg19::chr16:831621..831649,+p@chr16:831621..831649
+
Hg19::chr17:36003553..36003559,-p6@DDX52
Hg19::chr17:36068486..36068493,+p@chr17:36068486..36068493
+
Hg19::chr17:73554365..73554374,+p@chr17:73554365..73554374
+
Hg19::chr17:74128596..74128610,-p@chr17:74128596..74128610
-
Hg19::chr17:74134377..74134388,-p@chr17:74134377..74134388
-
Hg19::chr18:11959017..11959052,+p@chr18:11959017..11959052
+
Hg19::chr18:52274330..52274344,-p@chr18:52274330..52274344
-
Hg19::chr18:69246146..69246156,-p3@LOC100505776
Hg19::chr18:69246167..69246179,-p2@LOC100505776
Hg19::chr18:69246186..69246197,-p1@LOC100505776
Hg19::chr18:6982576..6982589,-p@chr18:6982576..6982589
-
Hg19::chr19:40697978..40698010,+p6@MAP3K10
Hg19::chr19:40762956..40762973,-p@chr19:40762956..40762973
-
Hg19::chr1:205601064..205601087,-p4@ELK4
Hg19::chr1:214650069..214650072,-p@chr1:214650069..214650072
-
Hg19::chr1:214650077..214650084,-p@chr1:214650077..214650084
-
Hg19::chr1:214650108..214650118,-p@chr1:214650108..214650118
-
Hg19::chr1:215257098..215257110,+p@chr1:215257098..215257110
+
Hg19::chr1:215257112..215257119,+p@chr1:215257112..215257119
+
Hg19::chr1:224370589..224370611,+p3@DEGS1
Hg19::chr1:46787487..46787492,-p@chr1:46787487..46787492
-
Hg19::chr1:46797583..46797614,-p@chr1:46797583..46797614
-
Hg19::chr1:94780142..94780153,-p@chr1:94780142..94780153
-
Hg19::chr1:94780176..94780187,-p@chr1:94780176..94780187
-
Hg19::chr20:15866720..15866725,-p@chr20:15866720..15866725
-
Hg19::chr20:15871874..15871910,-p@chr20:15871874..15871910
-
Hg19::chr20:15872559..15872568,-p@chr20:15872559..15872568
-
Hg19::chr20:15873011..15873014,-p@chr20:15873011..15873014
-
Hg19::chr20:15878694..15878728,-p@chr20:15878694..15878728
-
Hg19::chr20:15879525..15879530,-p@chr20:15879525..15879530
-
Hg19::chr20:15891295..15891297,-p@chr20:15891295..15891297
-
Hg19::chr20:15896547..15896555,-p@chr20:15896547..15896555
-
Hg19::chr20:15896790..15896803,-p@chr20:15896790..15896803
-
Hg19::chr20:15898490..15898493,-p@chr20:15898490..15898493
-
Hg19::chr20:15916678..15916682,-p@chr20:15916678..15916682
-
Hg19::chr20:15942024..15942025,-p@chr20:15942024..15942025
-
Hg19::chr20:15948322..15948327,-p@chr20:15948322..15948327
-
Hg19::chr20:15954227..15954237,-p@chr20:15954227..15954237
-
Hg19::chr20:15966439..15966448,-p@chr20:15966439..15966448
-
Hg19::chr20:15967531..15967544,+p@chr20:15967531..15967544
+
Hg19::chr20:15967629..15967655,+p@chr20:15967629..15967655
+
Hg19::chr20:15967658..15967661,+p@chr20:15967658..15967661
+
Hg19::chr20:15967691..15967705,+p@chr20:15967691..15967705
+
Hg19::chr20:58319374..58319386,-p@chr20:58319374..58319386
-
Hg19::chr20:60934189..60934206,-p@chr20:60934189..60934206
-
Hg19::chr20:60934239..60934260,-p@chr20:60934239..60934260
-
Hg19::chr20:62113538..62113571,-p@chr20:62113538..62113571
-
Hg19::chr21:44441260..44441273,+p3@PKNOX1
Hg19::chr22:31495739..31495756,+p33@SMTN
Hg19::chr22:31739255..31739259,-p28@PATZ1
Hg19::chr22:46812806..46812838,-p@chr22:46812806..46812838
-
Hg19::chr2:231906019..231906031,+p6@C2orf72
Hg19::chr2:239066313..239066357,+p@chr2:239066313..239066357
+
Hg19::chr2:28503793..28503800,+p@chr2:28503793..28503800
+
Hg19::chr2:31637816..31637836,-p7@XDH
Hg19::chr2:34902620..34902625,+p1@ENST00000423663
Hg19::chr2:34902895..34902908,+p1@uc002rpc.1
Hg19::chr2:34935472..34935477,+p@chr2:34935472..34935477
+
Hg19::chr2:34971950..34971953,+p@chr2:34971950..34971953
+
Hg19::chr3:168582660..168582692,+p@chr3:168582660..168582692
+
Hg19::chr3:168802151..168802153,-p@chr3:168802151..168802153
-
Hg19::chr3:168861573..168861582,-p@chr3:168861573..168861582
-
Hg19::chr3:168864427..168864464,-p19@MECOM
Hg19::chr3:168864831..168864851,-p9@MECOM
Hg19::chr3:168864936..168864953,-p8@MECOM
Hg19::chr3:168865144..168865160,-p6@MECOM
Hg19::chr3:168865250..168865272,-p5@MECOM
Hg19::chr3:168865278..168865292,-p14@MECOM
Hg19::chr3:168865323..168865337,-p15@MECOM
Hg19::chr3:168865364..168865376,-p11@MECOM
Hg19::chr3:168865497..168865516,-p16@MECOM
Hg19::chr4:135331403..135331405,-p@chr4:135331403..135331405
-
Hg19::chr4:135507221..135507238,-p@chr4:135507221..135507238
-
Hg19::chr4:159430869..159430885,-p1@ENST00000502566
Hg19::chr4:159442958..159442977,+p4@RXFP1
Hg19::chr4:159443003..159443018,+p3@RXFP1
Hg19::chr4:159443024..159443056,+p1@RXFP1
Hg19::chr4:159446395..159446403,+p@chr4:159446395..159446403
+
Hg19::chr4:159541085..159541093,+p@chr4:159541085..159541093
+
Hg19::chr4:175184004..175184014,-p16@FBXO8
Hg19::chr4:175184030..175184041,-p13@FBXO8
Hg19::chr4:175184051..175184061,-p18@FBXO8
Hg19::chr4:175184162..175184175,-p9@FBXO8
Hg19::chr4:175184180..175184194,-p2@FBXO8
Hg19::chr4:175184203..175184220,-p6@FBXO8
Hg19::chr4:175184241..175184250,-p14@FBXO8
Hg19::chr4:175204717..175204728,-p17@FBXO8
Hg19::chr4:25649638..25649642,+p@chr4:25649638..25649642
+
Hg19::chr5:175799252..175799262,-p@chr5:175799252..175799262
-
Hg19::chr5:31936363..31936370,+p19@PDZD2
Hg19::chr5:31936389..31936400,+p11@PDZD2
Hg19::chr5:36105527..36105539,-p@chr5:36105527..36105539
-
Hg19::chr6:137844183..137844191,-p@chr6:137844183..137844191
-
Hg19::chr6:13925318..13925342,+p2@RNF182
Hg19::chr6:14049473..14049508,+p@chr6:14049473..14049508
+
Hg19::chr6:24323980..24323989,-p@chr6:24323980..24323989
-
Hg19::chr6:47602833..47602848,+p@chr6:47602833..47602848
+
Hg19::chr6:64025774..64025778,-p@chr6:64025774..64025778
-
Hg19::chr6:64043904..64043907,-p@chr6:64043904..64043907
-
Hg19::chr6:64049378..64049403,-p@chr6:64049378..64049403
-
Hg19::chr6:64050722..64050726,-p@chr6:64050722..64050726
-
Hg19::chr6:64145806..64145815,-p@chr6:64145806..64145815
-
Hg19::chr6:64151611..64151636,-p@chr6:64151611..64151636
-
Hg19::chr6:64152250..64152255,-p@chr6:64152250..64152255
-
Hg19::chr6:72241518..72241524,+p@chr6:72241518..72241524
+
Hg19::chr6:75233360..75233363,+p@chr6:75233360..75233363
+
Hg19::chr7:107643719..107643730,-p9@LAMB1
Hg19::chr7:107644847..107644884,-p@chr7:107644847..107644884
-
Hg19::chr7:107707064..107707079,-p@chr7:107707064..107707079
-
Hg19::chr7:107707083..107707099,-p@chr7:107707083..107707099
-
Hg19::chr7:134627808..134627842,+p@chr7:134627808..134627842
+
Hg19::chr7:138816862..138816869,-p@chr7:138816862..138816869
-
Hg19::chr7:151791137..151791153,+p3@GALNT11
Hg19::chr7:151791485..151791495,+p15@GALNT11
Hg19::chr7:98735181..98735195,-p@chr7:98735181..98735195
-
Hg19::chr7:98735218..98735228,-p@chr7:98735218..98735228
-
Hg19::chr7:98735238..98735250,-p@chr7:98735238..98735250
-
Hg19::chr8:101363016..101363029,+p@chr8:101363016..101363029
+
Hg19::chr8:142247795..142247863,-p@chr8:142247795..142247863
-
Hg19::chr8:142247940..142247948,-p@chr8:142247940..142247948
-
Hg19::chr8:144124493..144124500,+p8@C8orf31
Hg19::chr8:144124531..144124572,+p2@C8orf31
Hg19::chr8:20070210..20070250,+p@chr8:20070210..20070250
+
Hg19::chr9:132472174..132472192,+p@chr9:132472174..132472192
+
Hg19::chr9:136856204..136856219,+p@chr9:136856204..136856219
+
Hg19::chr9:138466794..138466798,+p1@ENST00000445997
Hg19::chr9:90000420..90000454,-p@chr9:90000420..90000454
-
Hg19::chr9:90680465..90680480,-p1@uc004apv.1
Hg19::chrX:16329834..16329838,-p@chrX:16329834..16329838
-
Hg19::chrX:16422567..16422570,-p@chrX:16422567..16422570
-
Hg19::chrX:16530591..16530601,-p@chrX:16530591..16530601
-
Hg19::chrX:16530614..16530628,-p@chrX:16530614..16530628
-
Hg19::chrX:35711783..35711785,+p@chrX:35711783..35711785
+


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:0005515protein binding0.0291416460614624
GO:0004855xanthine oxidase activity0.0291416460614624
GO:0043257laminin-8 complex0.0291416460614624
GO:0005607laminin-2 complex0.0291416460614624
GO:0016727oxidoreductase activity, acting on CH or CH2 groups, oxygen as acceptor0.0291416460614624
GO:0016726oxidoreductase activity, acting on CH or CH2 groups, NAD or NADP as acceptor0.0364195514862496
GO:0004854xanthine dehydrogenase activity0.0364195514862496
GO:0043259laminin-10 complex0.0364195514862496
GO:0050794regulation of cellular process0.0436944567728137
GO:0004706JUN kinase kinase kinase activity0.0436944567728137
GO:0033559unsaturated fatty acid metabolic process0.0477161790289686
GO:0006636unsaturated fatty acid biosynthetic process0.0477161790289686
GO:0044424intracellular part0.0477161790289686
GO:0050789regulation of biological process0.0477161790289686
GO:0042803protein homodimerization activity0.0477161790289686



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
serous secreting cell9.37e-991
seromucus secreting cell2.74e-502
Uber Anatomy
Ontology termp-valuen
epithelium of female gonad9.37e-991
epithelium of gonad2.74e-502
female gonad5.28e-0913
Disease
Ontology termp-valuen
ovary epithelial cancer9.37e-991
clear cell adenocarcinoma4.52e-502
adenocarcinoma4.64e-1725
female reproductive organ cancer6.71e-1627
reproductive organ cancer6.74e-1529
ovarian cancer1.86e-0814


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)
MA0003.13.89415e-12
MA0004.10.0763001
MA0006.10.231152
MA0007.10.184958
MA0009.10.968844
MA0014.11.34419e-08
MA0017.10.191351
MA0019.10.185037
MA0024.10.202977
MA0025.10.0787174
MA0027.11.25654
MA0028.10.00533398
MA0029.10.0902786
MA0030.16.59475
MA0031.12.2911
MA0038.11.255
MA0040.11.45281
MA0041.10.75255
MA0042.10.0639018
MA0043.10.343883
MA0046.114.0949
MA0048.10.000394747
MA0050.10.119254
MA0051.10.00557062
MA0052.10.0960574
MA0055.10.0641429
MA0056.10
MA0057.10.00634798
MA0058.10.0660206
MA0059.10.495219
MA0060.10.0167024
MA0061.10.148852
MA0063.10
MA0066.10.0594838
MA0067.10.164163
MA0068.10.363724
MA0069.10.321452
MA0070.10.884723
MA0071.10.398645
MA0072.10.54906
MA0073.12.14937e-05
MA0074.10.343766
MA0076.10.00306838
MA0077.11.65942
MA0078.10.915906
MA0081.10.0648186
MA0083.13.63385
MA0084.10.767735
MA0087.13.29906
MA0088.10.0639589
MA0089.10
MA0090.10.665584
MA0091.10.0788916
MA0092.10.84745
MA0093.10.0387
MA0095.10
MA0098.10
MA0100.10.24941
MA0101.10.0414149
MA0103.10.380881
MA0105.10.0194452
MA0106.10.307461
MA0107.10.0679484
MA0108.20.285635
MA0109.10
MA0111.10.20015
MA0113.11.3179
MA0114.10.0936228
MA0115.10.786796
MA0116.10.227182
MA0117.10.179085
MA0119.10.552647
MA0122.10.777005
MA0124.10.344002
MA0125.10.915951
MA0130.10
MA0131.10.0239952
MA0132.10
MA0133.10
MA0135.11.07077
MA0136.10.376179
MA0139.10.000718776
MA0140.10.559205
MA0141.10.0330284
MA0142.10.937679
MA0143.11.319
MA0144.10.0421686
MA0145.10.00710554
MA0146.10.000413448
MA0147.10.0494701
MA0148.11.01296
MA0149.10.00259957
MA0062.20.000429287
MA0035.20.388226
MA0039.21.50825e-09
MA0138.20.0636621
MA0002.20.11325
MA0137.20.0567162
MA0104.20.00201565
MA0047.20.280909
MA0112.20.0331878
MA0065.20.198846
MA0150.10.477944
MA0151.10
MA0152.10.793929
MA0153.16.7933
MA0154.10.0108862
MA0155.10.0158035
MA0156.10.0994919
MA0157.11.86367
MA0158.10
MA0159.10.0804655
MA0160.10.477859
MA0161.10
MA0162.11.13468e-08
MA0163.13.15539e-08
MA0164.10.569537
MA0080.20.0387695
MA0018.20.181284
MA0099.20.163006
MA0079.20
MA0102.21.49759
MA0258.10.0324215
MA0259.10.00988558
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
CTBP2#1488104.046258086408270.000212176669014230.00246710299879505
ESR1#2099152.97760677059560.000176757459151850.00214905381564146



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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