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

Latest revision as of 10:33, 17 September 2013


Full id: C108_breast_hepatoblastoma_MCF7_parotid_salivary_submaxillary_prostate



Phase1 CAGE Peaks

Hg19::chr10:37451700..37451715,+p@chr10:37451700..37451715
+
Hg19::chr10:37451725..37451728,+p@chr10:37451725..37451728
+
Hg19::chr10:37485037..37485044,+p@chr10:37485037..37485044
+
Hg19::chr10:37485774..37485794,+p@chr10:37485774..37485794
+
Hg19::chr10:37555522..37555528,+p@chr10:37555522..37555528
+
Hg19::chr10:37555579..37555584,+p@chr10:37555579..37555584
+
Hg19::chr10:37601250..37601252,+p@chr10:37601250..37601252
+
Hg19::chr10:37637623..37637627,+p1@VN1R53P
Hg19::chr10:37656774..37656778,+p@chr10:37656774..37656778
+
Hg19::chr10:37679189..37679193,+p@chr10:37679189..37679193
+
Hg19::chr10:37685495..37685497,+p@chr10:37685495..37685497
+
Hg19::chr10:9062678..9062682,-p@chr10:9062678..9062682
-
Hg19::chr10:9102477..9102481,-p@chr10:9102477..9102481
-
Hg19::chr10:9107734..9107754,-p@chr10:9107734..9107754
-
Hg19::chr11:113212368..113212375,+p9@TTC12
Hg19::chr11:120110546..120110551,-p@chr11:120110546..120110551
-
Hg19::chr11:67436996..67437009,-p@chr11:67436996..67437009
-
Hg19::chr11:67437863..67437876,-p@chr11:67437863..67437876
-
Hg19::chr11:72493645..72493661,-p23@STARD10
Hg19::chr11:72493668..72493679,-p22@STARD10
Hg19::chr11:7618413..7618427,+p6@PPFIBP2
Hg19::chr11:7618431..7618436,+p34@PPFIBP2
Hg19::chr11:7618437..7618448,+p20@PPFIBP2
Hg19::chr11:827914..827930,+p15@EFCAB4A
Hg19::chr11:827941..827978,+p10@EFCAB4A
Hg19::chr11:828104..828109,+p32@EFCAB4A
Hg19::chr11:828151..828163,+p14@EFCAB4A
Hg19::chr11:829412..829430,+p11@EFCAB4A
Hg19::chr11:829495..829500,+p23@EFCAB4A
Hg19::chr11:829538..829547,+p17@EFCAB4A
Hg19::chr11:829560..829573,+p13@EFCAB4A
Hg19::chr11:830434..830484,+p1@EFCAB4A
Hg19::chr11:831114..831132,+p@chr11:831114..831132
+
Hg19::chr12:49453217..49453224,+p@chr12:49453217..49453224
+
Hg19::chr12:90313394..90313420,+p1@ENST00000549551
Hg19::chr12:93806120..93806155,-p@chr12:93806120..93806155
-
Hg19::chr14:46389767..46389768,+p@chr14:46389767..46389768
+
Hg19::chr14:76447439..76447452,-p18@TGFB3
Hg19::chr14:76447469..76447487,-p12@TGFB3
Hg19::chr14:92302549..92302564,-p9@TC2N
Hg19::chr15:69854027..69854040,+p1@LOC145837
Hg19::chr15:69857515..69857518,+p3@ENST00000559477
Hg19::chr15:69857547..69857555,+p1@ENST00000559477
Hg19::chr15:69857557..69857562,+p2@ENST00000559477
Hg19::chr16:48281411..48281419,-p5@ABCC11
Hg19::chr16:48281444..48281451,-p2@ABCC11
Hg19::chr16:54972581..54972585,-p1@ENST00000558156
p1@ENST00000559802
Hg19::chr17:12935401..12935405,-p@chr17:12935401..12935405
-
Hg19::chr17:61514114..61514119,-p@chr17:61514114..61514119
-
Hg19::chr17:61514163..61514170,-p@chr17:61514163..61514170
-
Hg19::chr17:61514195..61514205,-p@chr17:61514195..61514205
-
Hg19::chr17:61514208..61514213,-p@chr17:61514208..61514213
-
Hg19::chr17:65990349..65990362,-p@chr17:65990349..65990362
-
Hg19::chr17:65990378..65990389,-p@chr17:65990378..65990389
-
Hg19::chr17:65990392..65990397,-p@chr17:65990392..65990397
-
Hg19::chr17:65990543..65990553,-p@chr17:65990543..65990553
-
Hg19::chr17:72968809..72968834,-p1@C17orf28
Hg19::chr17:72968837..72968868,-p2@C17orf28
Hg19::chr17:73389834..73389850,-p4@GRB2
Hg19::chr18:20911185..20911195,-p6@TMEM241
Hg19::chr19:15674405..15674438,+p@chr19:15674405..15674438
+
Hg19::chr19:15674459..15674486,+p@chr19:15674459..15674486
+
Hg19::chr19:48010224..48010231,-p@chr19:48010224..48010231
-
Hg19::chr19:5217451..5217456,-p@chr19:5217451..5217456
-
Hg19::chr1:11139818..11139830,-p6@EXOSC10
Hg19::chr1:153940716..153940739,+p4@CREB3L4
Hg19::chr1:153940741..153940751,+p7@CREB3L4
Hg19::chr1:164559541..164559546,+p52@PBX1
Hg19::chr1:164559556..164559568,+p21@PBX1
Hg19::chr1:164559583..164559590,+p50@PBX1
Hg19::chr1:189493099..189493102,-p@chr1:189493099..189493102
-
Hg19::chr1:190446662..190446678,-p6@FAM5C
Hg19::chr1:190446698..190446710,-p10@FAM5C
Hg19::chr1:190447673..190447683,-p@chr1:190447673..190447683
-
Hg19::chr1:233750790..233750823,-p@chr1:233750790..233750823
-
Hg19::chr1:236686445..236686452,+p18@LGALS8
Hg19::chr1:236686501..236686513,+p8@LGALS8
Hg19::chr1:31882617..31882630,+p4@SERINC2
Hg19::chr1:40598486..40598500,+p1@ENST00000430724
Hg19::chr1:47366146..47366153,-p1@CYP4Z2P
Hg19::chr1:51763556..51763631,-p2@TTC39A
Hg19::chr1:53559544..53559570,-p@chr1:53559544..53559570
-
Hg19::chr1:53559600..53559623,-p@chr1:53559600..53559623
-
Hg19::chr1:86889165..86889168,+p@chr1:86889165..86889168
+
Hg19::chr1:86889531..86889552,+p4@CLCA2
Hg19::chr1:86911063..86911068,+p@chr1:86911063..86911068
+
Hg19::chr1:94080063..94080068,-p23@BCAR3
Hg19::chr1:94080175..94080205,-p@chr1:94080175..94080205
-
Hg19::chr20:31781321..31781329,+p2@BPIFA4P
Hg19::chr20:34380919..34380924,+p@chr20:34380919..34380924
+
Hg19::chr20:60803269..60803302,+p@chr20:60803269..60803302
+
Hg19::chr20:62173412..62173437,-p@chr20:62173412..62173437
-
Hg19::chr21:36729875..36729891,+p@chr21:36729875..36729891
+
Hg19::chr21:37505138..37505151,-p@chr21:37505138..37505151
-
Hg19::chr21:43540870..43540878,+p10@UMODL1
Hg19::chr21:43540892..43540907,+p4@UMODL1
Hg19::chr21:43540912..43540915,+p15@UMODL1
Hg19::chr21:47704051..47704065,-p11@MCM3AP
Hg19::chr21:47704085..47704094,-p18@MCM3AP
Hg19::chr22:24990735..24990742,+p8@GGT2
p9@GGT1
Hg19::chr22:46283597..46283636,-p1@ENST00000451118
Hg19::chr2:142889034..142889073,-p4@LRP1B
Hg19::chr2:142889081..142889086,-p11@LRP1B
Hg19::chr2:142895398..142895426,-p1@ENST00000436132
Hg19::chr2:149863976..149863986,+p@chr2:149863976..149863986
+
Hg19::chr2:149864004..149864021,+p@chr2:149864004..149864021
+
Hg19::chr2:242674815..242674830,-p3@ENST00000400768
Hg19::chr2:242680762..242680768,+p@chr2:242680762..242680768
+
Hg19::chr2:242680772..242680783,+p@chr2:242680772..242680783
+
Hg19::chr2:242680789..242680804,+p@chr2:242680789..242680804
+
Hg19::chr2:242681835..242681844,+p5@D2HGDH
Hg19::chr3:141174789..141174790,-p8@AK129571
Hg19::chr3:14833061..14833093,+p@chr3:14833061..14833093
+
Hg19::chr3:149002564..149002570,+p1@ENST00000489011
Hg19::chr3:169587753..169587760,-p3@LRRC31
Hg19::chr3:169756594..169756605,+p9@GPR160
Hg19::chr3:169756638..169756645,+p15@GPR160
Hg19::chr3:169756667..169756675,+p14@GPR160
Hg19::chr3:169756689..169756695,+p13@GPR160
Hg19::chr3:189026705..189026726,+p@chr3:189026705..189026726
+
Hg19::chr3:189438863..189438865,+p@chr3:189438863..189438865
+
Hg19::chr3:4722258..4722271,+p@chr3:4722258..4722271
+
Hg19::chr3:4722283..4722286,+p@chr3:4722283..4722286
+
Hg19::chr3:4722301..4722324,+p@chr3:4722301..4722324
+
Hg19::chr3:60761167..60761179,+p@chr3:60761167..60761179
+
Hg19::chr3:60761181..60761194,+p@chr3:60761181..60761194
+
Hg19::chr3:9956047..9956079,+p@chr3:9956047..9956079
+
Hg19::chr4:14879181..14879226,-p@chr4:14879181..14879226
-
Hg19::chr4:160605526..160605546,-p@chr4:160605526..160605546
-
Hg19::chr4:160605585..160605628,-p@chr4:160605585..160605628
-
Hg19::chr4:776378..776392,+p@chr4:776378..776392
+
Hg19::chr5:111755562..111755580,-p@chr5:111755562..111755580
-
Hg19::chr5:111755583..111755641,-p@chr5:111755583..111755641
-
Hg19::chr5:148231224..148231235,+p@chr5:148231224..148231235
+
Hg19::chr5:148231243..148231244,+p@chr5:148231243..148231244
+
Hg19::chr5:153666993..153667004,+p9@GALNT10
Hg19::chr5:153667008..153667036,+p3@GALNT10
Hg19::chr5:176513895..176513924,+p1@FGFR4
Hg19::chr5:176513938..176513951,+p3@FGFR4
Hg19::chr5:176514238..176514245,+p18@FGFR4
Hg19::chr5:176518002..176518011,+p19@FGFR4
Hg19::chr5:176519127..176519154,+p@chr5:176519127..176519154
+
Hg19::chr5:180022690..180022710,-p@chr5:180022690..180022710
-
Hg19::chr6:10141294..10141304,+p@chr6:10141294..10141304
+
Hg19::chr6:34524093..34524135,-p1@SPDEF
Hg19::chr6:44013424..44013453,-p@chr6:44013424..44013453
-
Hg19::chr6:50785214..50785224,+p@chr6:50785214..50785224
+
Hg19::chr6:50785279..50785289,+p@chr6:50785279..50785289
+
Hg19::chr6:50786414..50786426,+p7@TFAP2B
Hg19::chr6:50786479..50786490,+p6@TFAP2B
Hg19::chr6:50786509..50786527,+p5@TFAP2B
Hg19::chr6:50786529..50786540,+p8@TFAP2B
Hg19::chr6:50789717..50789729,+p4@TFAP2B
Hg19::chr6:50789737..50789746,+p10@TFAP2B
Hg19::chr6:50836577..50836581,+p@chr6:50836577..50836581
+
Hg19::chr7:157285832..157285841,+p@chr7:157285832..157285841
+
Hg19::chr7:42429365..42429366,-p@chr7:42429365..42429366
-
Hg19::chr7:42429373..42429374,-p@chr7:42429373..42429374
-
Hg19::chr7:42429377..42429382,-p@chr7:42429377..42429382
-
Hg19::chr7:94277045..94277057,-p@chr7:94277045..94277057
-
Hg19::chr8:116684676..116684688,-p@chr8:116684676..116684688
-
Hg19::chr8:30584492..30584503,-p10@GSR
Hg19::chr8:30584507..30584514,-p13@GSR
Hg19::chr8:30584524..30584529,-p14@GSR
Hg19::chr8:30584533..30584543,-p9@GSR
Hg19::chr8:58943424..58943435,+p@chr8:58943424..58943435
+
Hg19::chr8:58943437..58943442,+p@chr8:58943437..58943442
+
Hg19::chr9:117379097..117379106,+p3@AB528759
Hg19::chr9:131870403..131870416,-p@chr9:131870403..131870416
-
Hg19::chr9:131871258..131871269,-p3@CRAT
Hg19::chr9:131871491..131871519,+p@chr9:131871491..131871519
+
Hg19::chr9:140506839..140506847,+p9@ARRDC1
Hg19::chr9:140506865..140506902,+p5@ARRDC1
Hg19::chrX:153603404..153603411,-p127@FLNA
Hg19::chrX:153603415..153603426,-p119@FLNA
Hg19::chrX:153603428..153603446,-p104@FLNA
Hg19::chrX:153603570..153603573,-p@chrX:153603570..153603573
-
Hg19::chrX:66763970..66763981,+p7@AR


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:0006606protein import into nucleus0.0214404100491165
GO:0051170nuclear import0.0214404100491165
GO:0006749glutathione metabolic process0.0214404100491165
GO:0017038protein import0.0229499729418118
GO:0006913nucleocytoplasmic transport0.0314709153876722
GO:0051169nuclear transport0.0314709153876722
GO:0001655urogenital system development0.0320263746614859
GO:0051990(R)-2-hydroxyglutarate dehydrogenase activity0.0320263746614859
GO:0004092carnitine O-acetyltransferase activity0.0320263746614859
GO:0032025response to cobalt ion0.0320263746614859
GO:0010042response to manganese ion0.0320263746614859
GO:0004362glutathione-disulfide reductase activity0.0320263746614859
GO:0048702embryonic neurocranium morphogenesis0.0320263746614859
GO:0006605protein targeting0.0355748464990184
GO:0043565sequence-specific DNA binding0.0367617866652938
GO:0018685alkane 1-monooxygenase activity0.0499155661978534
GO:0042221response to chemical stimulus0.0499155661978534
GO:0006732coenzyme metabolic process0.0499155661978534
GO:0007167enzyme linked receptor protein signaling pathway0.0499155661978534
GO:0030850prostate gland development0.0499155661978534
GO:0015038glutathione disulfide oxidoreductase activity0.0499155661978534
GO:0015037peptide disulfide oxidoreductase activity0.0499155661978534
GO:0016413O-acetyltransferase activity0.0499155661978534
GO:0045817positive regulation of global transcription from RNA polymerase II promoter0.0499155661978534
GO:0000176nuclear exosome (RNase complex)0.0499155661978534



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
mammary gland epithelial cell3.10e-504
Uber Anatomy
Ontology termp-valuen
mammary gland3.10e-504
mammary bud3.10e-504
mammary ridge3.10e-504
mammary placode3.10e-504
external ectoderm5.22e-268
breast3.81e-2110
chest2.25e-1911
exocrine gland7.41e-0831
ectodermal placode7.41e-0831
exocrine system7.41e-0831
epithelial bud8.21e-0737
Disease
Ontology termp-valuen
thoracic cancer3.10e-504
breast cancer3.10e-504


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)
MA0003.15.33917e-05
MA0004.10.0382204
MA0006.11.3634
MA0007.10.254588
MA0009.10.493196
MA0014.11.20057e-05
MA0017.10.147413
MA0019.10.0551653
MA0024.10.0107507
MA0025.10.467777
MA0027.11.19827
MA0028.10.00401965
MA0029.10.163874
MA0030.11.11632
MA0031.11.50817
MA0038.10.138842
MA0040.10.852914
MA0041.11.10193
MA0042.12.1592
MA0043.10.493869
MA0046.10.758809
MA0048.10.143606
MA0050.10.528368
MA0051.10.133011
MA0052.10.0661032
MA0055.10.00542313
MA0056.10
MA0057.10.024001
MA0058.10.0287331
MA0059.10.295979
MA0060.10.116008
MA0061.10.106096
MA0063.10
MA0066.10.717874
MA0067.10.133805
MA0068.12.29248
MA0069.12.99505
MA0070.10.714582
MA0071.10.161451
MA0072.10.225438
MA0073.11.9273e-06
MA0074.10.131988
MA0076.10.0390581
MA0077.10.415001
MA0078.10.310446
MA0081.10.528654
MA0083.10.0270626
MA0084.10.677234
MA0087.10.425426
MA0088.10.173976
MA0089.10
MA0090.10.425396
MA0091.10.00178301
MA0092.10.00862013
MA0093.10.0269594
MA0095.10
MA0098.10
MA0100.10.264939
MA0101.10.0291277
MA0103.12.68631
MA0105.10.27208
MA0106.10.0528231
MA0107.10.00324851
MA0108.20.574977
MA0109.10
MA0111.10.0631887
MA0113.11.60895
MA0114.10.302781
MA0115.10.0987273
MA0116.10.0262156
MA0117.10.315887
MA0119.12.85438
MA0122.10.354237
MA0124.10.27982
MA0125.11.64129
MA0130.10
MA0131.10.0133298
MA0132.10
MA0133.10
MA0135.12.22245
MA0136.10.550177
MA0139.10.137179
MA0140.10.532095
MA0141.10.289593
MA0142.10.305174
MA0143.10.234178
MA0144.10.990778
MA0145.11.07579
MA0146.10.00534803
MA0147.10.110453
MA0148.13.39366
MA0149.10.0152538
MA0062.20.00325236
MA0035.20.155827
MA0039.20.0012455
MA0138.20.313167
MA0002.20.118211
MA0137.20.0707026
MA0104.20.113746
MA0047.24.63406
MA0112.21.48574
MA0065.20.215068
MA0150.10.010265
MA0151.10
MA0152.10.268938
MA0153.10.722082
MA0154.10.962877
MA0155.10.680557
MA0156.10.173323
MA0157.11.50473
MA0158.10
MA0159.10.289664
MA0160.10.124312
MA0161.10
MA0162.11.81553e-06
MA0163.10.000420675
MA0164.10.146911
MA0080.20.436193
MA0018.20.0536492
MA0099.20.0197344
MA0079.25.22072e-10
MA0102.20.733957
MA0258.11.17972
MA0259.10.250666
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
EP300#2033451.712513357753060.0001652880030192290.00203351557866949
ESR1#2099132.247145184550610.005743764701949730.0258755571628748
FOXA1#3169493.050503189437578.75118373867725e-131.23675896953141e-10
GATA3#2625416.273579610367683.32876033620379e-218.89136574815314e-19



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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