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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 10:32, 17 September 2013


Full id: C106_Hep2_epitheloid_placenta_cervical_rectal_anaplastic_glassy



Phase1 CAGE Peaks

Hg19::chr10:47079076..47079087,+p@chr10:47079076..47079087
+
Hg19::chr11:125821678..125821700,+p1@ENST00000531193
p1@uc001qda.2
Hg19::chr11:2008416..2008424,-p@chr11:2008416..2008424
-
Hg19::chr11:3147806..3147811,-p7@OSBPL5
Hg19::chr11:3147835..3147866,-p2@OSBPL5
Hg19::chr11:3147868..3147894,-p3@OSBPL5
Hg19::chr11:3147896..3147911,-p5@OSBPL5
Hg19::chr11:3829763..3829832,+p2@PGAP2
Hg19::chr11:4116005..4116047,+p2@RRM1
Hg19::chr11:4116054..4116105,+p1@RRM1
Hg19::chr11:4116108..4116133,+p3@RRM1
Hg19::chr11:4128664..4128687,+p@chr11:4128664..4128687
+
Hg19::chr11:4142834..4142878,+p5@RRM1
Hg19::chr11:4154830..4154835,+p@chr11:4154830..4154835
+
Hg19::chr11:66742742..66742753,+p3@C11orf86
Hg19::chr12:51923800..51923807,+p@chr12:51923800..51923807
+
Hg19::chr12:9297545..9297579,+p@chr12:9297545..9297579
+
Hg19::chr13:107315737..107315759,+p1@ATP5G1P5
Hg19::chr14:100873293..100873312,+p1@ENST00000556411
Hg19::chr14:101034469..101034487,-p8@BEGAIN
Hg19::chr16:2867130..2867141,+p3@PRSS21
Hg19::chr16:2867201..2867209,+p2@PRSS21
Hg19::chr16:2867213..2867220,+p4@PRSS21
Hg19::chr16:2867231..2867246,+p1@PRSS21
Hg19::chr16:2867406..2867433,+p@chr16:2867406..2867433
+
Hg19::chr16:2867643..2867681,+p@chr16:2867643..2867681
+
Hg19::chr16:81040722..81040749,-p4@C16orf61
Hg19::chr16:87869840..87869849,+p@chr16:87869840..87869849
+
Hg19::chr16:87869864..87869878,+p@chr16:87869864..87869878
+
Hg19::chr16:87870800..87870828,-p@chr16:87870800..87870828
-
Hg19::chr16:87872769..87872797,-p@chr16:87872769..87872797
-
Hg19::chr16:87874486..87874492,-p@chr16:87874486..87874492
-
Hg19::chr17:79098633..79098647,-p@chr17:79098633..79098647
-
Hg19::chr17:9745568..9745583,+p8@GLP2R
Hg19::chr17:9745786..9745816,+p2@GLP2R
Hg19::chr17:9745823..9745837,+p4@GLP2R
Hg19::chr17:9745841..9745870,+p1@GLP2R
Hg19::chr18:33077964..33078002,-p2@INO80C
Hg19::chr18:48176351..48176356,+p@chr18:48176351..48176356
+
Hg19::chr18:48176398..48176416,+p@chr18:48176398..48176416
+
Hg19::chr18:51686438..51686469,-p@chr18:51686438..51686469
-
Hg19::chr19:3603267..3603275,+p@chr19:3603267..3603275
+
Hg19::chr19:3603296..3603307,+p@chr19:3603296..3603307
+
Hg19::chr19:52646236..52646246,+p2@ENST00000492641
Hg19::chr1:207262150..207262161,+p9@C4BPB
Hg19::chr1:207262170..207262212,+p1@C4BPB
Hg19::chr1:207262215..207262226,+p4@C4BPB
Hg19::chr1:207262232..207262254,+p2@C4BPB
Hg19::chr1:207262293..207262306,+p17@C4BPB
Hg19::chr1:207262478..207262493,+p14@C4BPB
Hg19::chr1:207262814..207262825,+p15@C4BPB
Hg19::chr1:207262856..207262880,+p8@C4BPB
Hg19::chr1:207263488..207263499,+p@chr1:207263488..207263499
+
Hg19::chr1:207263514..207263528,+p@chr1:207263514..207263528
+
Hg19::chr1:207263643..207263662,+p@chr1:207263643..207263662
+
Hg19::chr1:225653027..225653052,-p1@ENST00000428642
Hg19::chr21:42608536..42608555,+p12@BACE2
Hg19::chr21:44561726..44561765,-p@chr21:44561726..44561765
-
Hg19::chr21:44816823..44816837,-p@chr21:44816823..44816837
-
Hg19::chr21:46470677..46470687,-p@chr21:46470677..46470687
-
Hg19::chr2:121669351..121669360,-p@chr2:121669351..121669360
-
Hg19::chr2:20650796..20650830,+p1@ENST00000448241
Hg19::chr2:211421073..211421089,+p9@CPS1
Hg19::chr2:211427642..211427670,+p@chr2:211427642..211427670
+
Hg19::chr2:211469821..211469857,+p8@CPS1
Hg19::chr2:211543115..211543126,+p@chr2:211543115..211543126
+
Hg19::chr2:218871722..218871728,+p@chr2:218871722..218871728
+
Hg19::chr2:226378168..226378193,+p@chr2:226378168..226378193
+
Hg19::chr2:226378208..226378213,+p@chr2:226378208..226378213
+
Hg19::chr2:233243233..233243245,+p5@ALPP
Hg19::chr2:233243424..233243433,+p2@ALPP
Hg19::chr2:233243453..233243468,+p1@ALPP
Hg19::chr2:233243964..233243976,+p@chr2:233243964..233243976
+
Hg19::chr2:233244473..233244503,+p1@AK297894
Hg19::chr2:233244912..233244922,+p2@AK297894
Hg19::chr2:233246427..233246435,+p18@ALPP
Hg19::chr2:233246442..233246451,+p16@ALPP
Hg19::chr2:233246459..233246472,+p9@ALPP
Hg19::chr2:233246540..233246555,+p7@ALPP
Hg19::chr2:233246589..233246598,+p12@ALPP
Hg19::chr2:233246656..233246666,+p8@ALPP
Hg19::chr2:233246764..233246778,+p3@ALPP
Hg19::chr2:233246793..233246841,-p1@ENST00000441266
Hg19::chr2:233246828..233246839,+p4@ALPP
Hg19::chr2:233246932..233246943,+p6@ALPP
Hg19::chr2:233246988..233246995,+p@chr2:233246988..233246995
+
Hg19::chr2:233321333..233321358,+p@chr2:233321333..233321358
+
Hg19::chr2:233323834..233323845,+p@chr2:233323834..233323845
+
Hg19::chr2:233324172..233324183,+p@chr2:233324172..233324183
+
Hg19::chr2:233324211..233324229,-p@chr2:233324211..233324229
-
Hg19::chr2:238592039..238592054,+p4@LRRFIP1
Hg19::chr2:53732986..53732989,-p@chr2:53732986..53732989
-
Hg19::chr2:99389915..99389917,+p@chr2:99389915..99389917
+
Hg19::chr3:125775961..125775982,-p4@SLC41A3
Hg19::chr3:125775994..125776003,-p13@SLC41A3
Hg19::chr3:127395141..127395157,+p3@ABTB1
Hg19::chr3:4637757..4637784,+p7@ITPR1
Hg19::chr3:4637817..4637826,+p12@ITPR1
Hg19::chr4:123838984..123838995,-p@chr4:123838984..123838995
-
Hg19::chr4:123839002..123839016,-p@chr4:123839002..123839016
-
Hg19::chr4:134183951..134183960,-p4@ENST00000507172
Hg19::chr4:134184041..134184064,-p2@ENST00000507172
Hg19::chr4:134184268..134184272,-p1@ENST00000507172
Hg19::chr4:24322838..24322853,-p@chr4:24322838..24322853
-
Hg19::chr4:24323064..24323083,+p@chr4:24323064..24323083
+
Hg19::chr5:147582333..147582347,+p2@SPINK6
Hg19::chr5:147582348..147582361,+p5@SPINK6
Hg19::chr5:147582387..147582396,+p7@SPINK6
Hg19::chr5:147582412..147582423,+p9@SPINK6
Hg19::chr5:147582427..147582438,+p6@SPINK6
Hg19::chr5:147582468..147582479,+p3@SPINK6
Hg19::chr5:147582537..147582549,+p4@SPINK6
Hg19::chr5:147582568..147582578,+p8@SPINK6
Hg19::chr5:147582587..147582659,+p1@SPINK6
Hg19::chr5:147648268..147648281,+p2@SPINK13
Hg19::chr5:147648290..147648301,+p4@SPINK13
Hg19::chr5:147648304..147648364,+p1@SPINK13
Hg19::chr5:147648393..147648403,+p3@SPINK13
Hg19::chr5:17216221..17216259,-p@chr5:17216221..17216259
-
Hg19::chr5:37249111..37249143,+p@chr5:37249111..37249143
+
Hg19::chr6:64273353..64273372,+p@chr6:64273353..64273372
+
Hg19::chr6:64281927..64281943,+p17@PTP4A1
Hg19::chr6:64281946..64281977,+p12@PTP4A1
Hg19::chr6:64282122..64282131,+p40@PTP4A1
Hg19::chr6:64282212..64282247,+p19@PTP4A1
Hg19::chr7:100100722..100100732,-p@chr7:100100722..100100732
-
Hg19::chr7:158766986..158767004,+p@chr7:158766986..158767004
+
Hg19::chr7:54879745..54879759,-p@chr7:54879745..54879759
-
Hg19::chr7:54879785..54879794,-p@chr7:54879785..54879794
-
Hg19::chr7:54879818..54879835,-p@chr7:54879818..54879835
-
Hg19::chr7:54879838..54879849,-p@chr7:54879838..54879849
-
Hg19::chr8:101349850..101349862,+p1@ENST00000519566
Hg19::chr8:128231080..128231222,-p1@ENST00000500112
p1@uc003ysa.1
Hg19::chr8:128231226..128231265,-p2@ENST00000500112
p2@uc003ysa.1
Hg19::chr8:128231266..128231291,-p7@ENST00000500112
p7@uc003ysa.1
Hg19::chr8:128231299..128231352,-p3@ENST00000500112
p3@uc003ysa.1
Hg19::chr8:128231366..128231373,-p12@ENST00000500112
p12@uc003ysa.1
Hg19::chr8:128231385..128231401,-p8@ENST00000500112
p8@uc003ysa.1
Hg19::chr8:128231407..128231419,-p10@ENST00000500112
p10@uc003ysa.1
Hg19::chr8:128231438..128231455,-p6@ENST00000500112
p6@uc003ysa.1
Hg19::chr8:128231456..128231465,-p13@ENST00000500112
p13@uc003ysa.1
Hg19::chr8:128231471..128231489,-p4@ENST00000500112
p4@uc003ysa.1
Hg19::chr8:128231499..128231515,-p5@ENST00000500112
p5@uc003ysa.1
Hg19::chr8:128231669..128231680,-p9@ENST00000500112
p9@uc003ysa.1
Hg19::chr8:128231737..128231742,-p14@ENST00000500112
p14@uc003ysa.1
Hg19::chr8:128231755..128231758,-p11@ENST00000500112
p11@uc003ysa.1
Hg19::chr8:128232038..128232051,-p@chr8:128232038..128232051
-
Hg19::chr8:128232069..128232086,-p@chr8:128232069..128232086
-
Hg19::chr8:128235084..128235088,-p@chr8:128235084..128235088
-
Hg19::chr8:128238982..128239007,-p@chr8:128238982..128239007
-
Hg19::chr8:128239211..128239226,-p@chr8:128239211..128239226
-
Hg19::chr8:128240919..128240940,-p2@uc003ysb.2
Hg19::chr8:128241017..128241070,-p1@uc003ysb.2
Hg19::chr8:128241079..128241090,-p5@uc003ysb.2
Hg19::chr8:128241092..128241104,-p3@uc003ysb.2
Hg19::chr8:128241150..128241167,-p4@uc003ysb.2
Hg19::chr8:128241234..128241241,-p7@uc003ysb.2
Hg19::chr8:128265552..128265583,-p@chr8:128265552..128265583
-
Hg19::chr8:128433201..128433228,-p1@ENST00000501396
p1@ENST00000523825
p1@uc003ysc.1
p1@uc003ysd.1
Hg19::chr8:143781405..143781425,+p5@LY6K
Hg19::chr8:143781432..143781443,+p7@LY6K
Hg19::chr8:143781490..143781507,+p4@LY6K
Hg19::chr8:143781830..143781881,+p2@LY6K
Hg19::chr8:143781883..143781895,+p6@LY6K
Hg19::chr8:143781901..143781949,+p3@LY6K
Hg19::chr8:143782507..143782516,+p@chr8:143782507..143782516
+
Hg19::chr8:40071801..40071804,-p@chr8:40071801..40071804
-
Hg19::chr9:124088884..124088895,+p15@GSN
Hg19::chr9:124088907..124088937,+p5@GSN
Hg19::chr9:124088949..124088972,+p11@GSN
Hg19::chr9:133710199..133710220,-p@chr9:133710199..133710220
-
Hg19::chr9:33443566..33443587,-p16@AQP3
Hg19::chr9:84380797..84380800,+p@chr9:84380797..84380800
+
Hg19::chr9:9085941..9085944,+p@chr9:9085941..9085944
+
Hg19::chrX:115594126..115594143,-p1@CXorf61
Hg19::chrX:115594160..115594172,-p2@CXorf61
Hg19::chrX:115594195..115594200,-p3@CXorf61
Hg19::chrX:86868584..86868590,+p@chrX:86868584..86868590
+
Hg19::chrX:86868675..86868686,+p@chrX:86868675..86868686
+


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:0005886plasma membrane0.0440502824122341
GO:0005971ribonucleoside-diphosphate reductase complex0.0440502824122341
GO:0004087carbamoyl-phosphate synthase (ammonia) activity0.0440502824122341
GO:0046903secretion0.0440502824122341
GO:0008142oxysterol binding0.0440502824122341
GO:0004086carbamoyl-phosphate synthase activity0.0440502824122341
GO:0042985negative regulation of amyloid precursor protein biosynthetic process0.0440502824122341
GO:0005737cytoplasm0.0440502824122341
GO:0048503GPI anchor binding0.0440502824122341
GO:0042984regulation of amyloid precursor protein biosynthetic process0.0440502824122341
GO:0005220inositol 1,4,5-triphosphate-sensitive calcium-release channel activity0.0440502824122341
GO:0042983amyloid precursor protein biosynthetic process0.0440502824122341
GO:0051014actin filament severing0.0440502824122341
GO:0008095inositol-1,4,5-triphosphate receptor activity0.0440502824122341
GO:0004035alkaline phosphatase activity0.0440502824122341
GO:0009049aspartic-type signal peptidase activity0.0458742318234648
GO:0016728oxidoreductase activity, acting on CH or CH2 groups, disulfide as acceptor0.0458742318234648
GO:0004748ribonucleoside-diphosphate reductase activity0.0458742318234648



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
epithelial cell1.34e-07253
Uber Anatomy
Ontology termp-valuen
larynx1.39e-1369
upper respiratory tract1.70e-6419
respiratory primordium5.59e-3238
endoderm of foregut5.59e-3238
segment of respiratory tract9.82e-2647
respiratory tract2.60e-2254
respiratory system4.37e-1674
foregut1.45e-1387
organ segment5.94e-1298
subdivision of digestive tract1.08e-09118
digestive system9.76e-08145
digestive tract9.76e-08145
primitive gut9.76e-08145
primordium5.59e-07160
endoderm-derived structure6.26e-07160
endoderm6.26e-07160
presumptive endoderm6.26e-07160
Disease
Ontology termp-valuen
carcinoma9.85e-20106
cell type cancer2.34e-14143
cancer7.82e-10235
disease of cellular proliferation1.33e-09239


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)
MA0003.10.0171593
MA0004.10.0370559
MA0006.10.0709603
MA0007.10.358024
MA0009.11.14356
MA0014.11.24975e-07
MA0017.10.806812
MA0019.10.33483
MA0024.10.0105262
MA0025.10.0582445
MA0027.11.19591
MA0028.10.00141015
MA0029.10.0605513
MA0030.10.784886
MA0031.10.365602
MA0038.10.0311453
MA0040.10.844999
MA0041.10.0490172
MA0042.10.107058
MA0043.10.107327
MA0046.10.100294
MA0048.10.0303323
MA0050.10.0607352
MA0051.10.0674932
MA0052.10.340178
MA0055.10.0690158
MA0056.10
MA0057.10.461694
MA0058.10.0516585
MA0059.10.289174
MA0060.11.08798e-08
MA0061.10.0329573
MA0063.10
MA0066.10.357891
MA0067.10.82103
MA0068.10.0261384
MA0069.10.457574
MA0070.11.43272
MA0071.11.17283
MA0072.10.0886887
MA0073.12.74072e-07
MA0074.11.42376
MA0076.10.0377179
MA0077.10.213495
MA0078.10.473919
MA0081.10.0864233
MA0083.10.111991
MA0084.10.239747
MA0087.10.420943
MA0088.10.000562748
MA0089.10
MA0090.17.11057
MA0091.10.131433
MA0092.10.910791
MA0093.10.00622769
MA0095.10
MA0098.10
MA0100.10.260293
MA0101.10.00102472
MA0103.10.0346618
MA0105.10.0104424
MA0106.10.0515862
MA0107.10.012545
MA0108.20.092748
MA0109.10
MA0111.10.479134
MA0113.11.28064
MA0114.10.583629
MA0115.10.663315
MA0116.13.12485
MA0117.10.132733
MA0119.11.47429
MA0122.10.152175
MA0124.12.01754
MA0125.10.75878
MA0130.10
MA0131.10.0439662
MA0132.10
MA0133.10
MA0135.10.302319
MA0136.10.37727
MA0139.10.979536
MA0140.10.0172105
MA0141.10.385648
MA0142.10.0236847
MA0143.10.0618949
MA0144.10.694091
MA0145.16.19477
MA0146.10.0550191
MA0147.10.0276382
MA0148.10.533231
MA0149.10.0764271
MA0062.20.000703424
MA0035.20.246451
MA0039.20.000287155
MA0138.20.47765
MA0002.21.29094
MA0137.21.00787
MA0104.20.020929
MA0047.20.445524
MA0112.22.32906
MA0065.20.350634
MA0150.10.283598
MA0151.10
MA0152.10.263921
MA0153.10.716336
MA0154.14.25701
MA0155.10.0466418
MA0156.10.0713468
MA0157.10.870595
MA0158.10
MA0159.10.571792
MA0160.11.80979
MA0161.10
MA0162.11.7327e-07
MA0163.10.00474872
MA0164.10.253842
MA0080.20.678105
MA0018.20.111598
MA0099.21.20351
MA0079.20
MA0102.21.343
MA0258.10.854615
MA0259.10.127398
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#1051542.404703753042124.06212876468436e-103.9985359665869e-08
FOSL2#2355312.932045914756497.26319825399255e-084.37463184803188e-06
FOXA1#3169291.795313814146250.001484464106766640.0094945156988549
FOXA2#3170243.302408547843393.24390269546618e-071.62411291280821e-05
HNF4A#3172151.938460086281040.01137190767361630.0416843558024992
HSF1#329765.506949720670390.0008637083421908380.00644688647441887
JUN#3725292.027218137305890.000213952058701370.00246578449114019
MAFF#23764134.089942091448532.21706379923969e-050.000485527209328567
NR3C1#2908594.935242327034691.44675746748054e-254.70709978648598e-23
POLR3A#1112847.578371175234480.002058769456999480.0119493066199605
PPARGC1A#108911121.51152234636876.70060773439591e-128.55507055223196e-10
RXRA#6256212.355122681127370.0002537231829304950.00273125082478643
SMC3#9126211.765047987394360.008271542491760130.032591550075339
STAT1#6772182.082226675696010.002757800926865440.0151224388848524
STAT3#6774301.76303882633870.001616231932449080.0101270486436914
TCF7L2#6934352.105900445306181.92729178064124e-050.000435303690048421
TFAP2A#7020312.860769081365331.24970262278798e-077.1634298694486e-06
TFAP2C#7022342.053149568353344.33170017792139e-050.000772274555960963



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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