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{{Coexpression_clusters
{
|full_id=C122_chronic_Reticulocytes_skeletal_leukemia_acute_colon_Tracheal
|

Latest revision as of 10:36, 17 September 2013


Full id: C122_chronic_Reticulocytes_skeletal_leukemia_acute_colon_Tracheal



Phase1 CAGE Peaks

Hg19::chr10:1205766..1205784,+p1@LINC00200
Hg19::chr10:133812422..133812433,-p@chr10:133812422..133812433
-
Hg19::chr10:23344774..23344789,-p@chr10:23344774..23344789
-
Hg19::chr10:32261513..32261517,-p@chr10:32261513..32261517
-
Hg19::chr10:74386276..74386278,+p@chr10:74386276..74386278
+
Hg19::chr10:7706496..7706498,-p@chr10:7706496..7706498
-
Hg19::chr11:107123494..107123497,-p@chr11:107123494..107123497
-
Hg19::chr11:12786182..12786188,+p@chr11:12786182..12786188
+
Hg19::chr11:66636028..66636036,-p@chr11:66636028..66636036
-
Hg19::chr11:73499170..73499182,-p@chr11:73499170..73499182
-
Hg19::chr11:74857404..74857406,-p@chr11:74857404..74857406
-
Hg19::chr12:127384780..127384784,-p@chr12:127384780..127384784
-
Hg19::chr12:131484807..131484812,+p@chr12:131484807..131484812
+
Hg19::chr12:40834251..40834284,+p@chr12:40834251..40834284
+
Hg19::chr12:40834308..40834315,+p@chr12:40834308..40834315
+
Hg19::chr12:56360072..56360078,+p6@CDK2
Hg19::chr12:83544470..83544473,-p@chr12:83544470..83544473
-
Hg19::chr14:21288539..21288543,-p@chr14:21288539..21288543
-
Hg19::chr14:21288980..21288985,+p@chr14:21288980..21288985
+
Hg19::chr14:57476704..57476716,+p@chr14:57476704..57476716
+
Hg19::chr15:29741976..29741979,-p@chr15:29741976..29741979
-
Hg19::chr15:31292147..31292151,-p@chr15:31292147..31292151
-
Hg19::chr15:55529745..55529773,-p@chr15:55529745..55529773
-
Hg19::chr15:56614511..56614514,+p@chr15:56614511..56614514
+
Hg19::chr15:58838947..58838952,+p@chr15:58838947..58838952
+
Hg19::chr16:15776378..15776383,+p@chr16:15776378..15776383
+
Hg19::chr16:18944204..18944211,-p@chr16:18944204..18944211
-
Hg19::chr16:202850..202864,+p1@HBZ
Hg19::chr16:204428..204475,+p@chr16:204428..204475
+
Hg19::chr16:3032177..3032182,-p@chr16:3032177..3032182
-
Hg19::chr16:57717053..57717056,-p@chr16:57717053..57717056
-
Hg19::chr16:85602486..85602494,+p@chr16:85602486..85602494
+
Hg19::chr16:87808740..87808748,-p@chr16:87808740..87808748
-
Hg19::chr17:42607348..42607359,+p@chr17:42607348..42607359
+
Hg19::chr17:45253914..45253921,+p@chr17:45253914..45253921
+
Hg19::chr17:47841886..47841889,-p9@FAM117A
Hg19::chr17:56743816..56743819,-p@chr17:56743816..56743819
-
Hg19::chr17:56744054..56744060,-p1@ENST00000362556
Hg19::chr17:68125012..68125027,-p1@ENST00000435112
Hg19::chr17:74438976..74438981,-p@chr17:74438976..74438981
-
Hg19::chr17:79323902..79323907,-p@chr17:79323902..79323907
-
Hg19::chr18:57647728..57647732,+p@chr18:57647728..57647732
+
Hg19::chr18:74587496..74587504,+p@chr18:74587496..74587504
+
Hg19::chr18:9014300..9014305,-p@chr18:9014300..9014305
-
Hg19::chr19:10949257..10949260,-p@chr19:10949257..10949260
-
Hg19::chr19:17377560..17377565,-p@chr19:17377560..17377565
-
Hg19::chr19:38993672..38993677,-p@chr19:38993672..38993677
-
Hg19::chr19:42751534..42751542,-p@chr19:42751534..42751542
-
Hg19::chr19:436927..436931,-p@chr19:436927..436931
-
Hg19::chr19:46440375..46440384,-p@chr19:46440375..46440384
-
Hg19::chr19:49467870..49467873,+p@chr19:49467870..49467873
+
Hg19::chr19:5434724..5434729,-p@chr19:5434724..5434729
-
Hg19::chr19:5435171..5435175,+p@chr19:5435171..5435175
+
Hg19::chr1:100113372..100113376,-p@chr1:100113372..100113376
-
Hg19::chr1:155804252..155804267,-p@chr1:155804252..155804267
-
Hg19::chr1:16158432..16158434,-p@chr1:16158432..16158434
-
Hg19::chr1:185126828..185126842,+p@chr1:185126828..185126842
+
Hg19::chr1:21055891..21055895,+p@chr1:21055891..21055895
+
Hg19::chr1:230875702..230875707,-p@chr1:230875702..230875707
-
Hg19::chr1:245725174..245725179,+p@chr1:245725174..245725179
+
Hg19::chr1:247268412..247268417,+p@chr1:247268412..247268417
+
Hg19::chr1:25215144..25215151,+p@chr1:25215144..25215151
+
Hg19::chr1:27392741..27392745,+p@chr1:27392741..27392745
+
Hg19::chr1:46503176..46503184,+p@chr1:46503176..46503184
+
Hg19::chr1:65946823..65946834,-p@chr1:65946823..65946834
-
Hg19::chr20:57596336..57596338,-p@chr20:57596336..57596338
-
Hg19::chr21:15825365..15825368,+p@chr21:15825365..15825368
+
Hg19::chr21:16572678..16572681,+p@chr21:16572678..16572681
+
Hg19::chr21:33889412..33889416,+p@chr21:33889412..33889416
+
Hg19::chr21:40277730..40277733,+p@chr21:40277730..40277733
+
Hg19::chr21:46587991..46587996,+p@chr21:46587991..46587996
+
Hg19::chr22:19678914..19678918,-p@chr22:19678914..19678918
-
Hg19::chr22:20188191..20188215,+p@chr22:20188191..20188215
+
Hg19::chr22:20255641..20255651,-p8@RTN4R
Hg19::chr22:30605270..30605275,+p@chr22:30605270..30605275
+
Hg19::chr22:39835764..39835768,+p@chr22:39835764..39835768
+
Hg19::chr2:106217257..106217261,-p@chr2:106217257..106217261
-
Hg19::chr2:108972782..108972789,+p@chr2:108972782..108972789
+
Hg19::chr2:119972623..119972627,+p@chr2:119972623..119972627
+
Hg19::chr2:136006392..136006395,-p@chr2:136006392..136006395
-
Hg19::chr2:145116694..145116698,+p@chr2:145116694..145116698
+
Hg19::chr2:152685303..152685308,+p@chr2:152685303..152685308
+
Hg19::chr2:169310156..169310163,-p@chr2:169310156..169310163
-
Hg19::chr2:180658273..180658279,+p@chr2:180658273..180658279
+
Hg19::chr2:181848643..181848652,+p20@UBE2E3
Hg19::chr2:217785498..217785504,-p@chr2:217785498..217785504
-
Hg19::chr2:226321257..226321288,-p@chr2:226321257..226321288
-
Hg19::chr2:241721829..241721844,-p@chr2:241721829..241721844
-
Hg19::chr2:54816567..54816573,-p@chr2:54816567..54816573
-
Hg19::chr2:70944889..70944893,+p@chr2:70944889..70944893
+
Hg19::chr2:8820960..8820963,-p@chr2:8820960..8820963
-
Hg19::chr2:8820995..8821000,-p@chr2:8820995..8821000
-
Hg19::chr3:128740865..128740872,+p@chr3:128740865..128740872
+
Hg19::chr3:13044317..13044322,-p@chr3:13044317..13044322
-
Hg19::chr3:138582577..138582582,+p@chr3:138582577..138582582
+
Hg19::chr3:156322310..156322314,-p@chr3:156322310..156322314
-
Hg19::chr3:193660436..193660439,+p@chr3:193660436..193660439
+
Hg19::chr3:197833253..197833259,+p@chr3:197833253..197833259
+
Hg19::chr3:25634199..25634205,-p@chr3:25634199..25634205
-
Hg19::chr3:37000324..37000332,+p@chr3:37000324..37000332
+
Hg19::chr3:49507014..49507019,-p@chr3:49507014..49507019
-
Hg19::chr3:65013149..65013151,-p@chr3:65013149..65013151
-
Hg19::chr3:65561104..65561130,-p@chr3:65561104..65561130
-
Hg19::chr4:127566945..127566951,-p@chr4:127566945..127566951
-
Hg19::chr4:13532999..13533030,-p1@LOC285547
Hg19::chr4:138399813..138399819,+p@chr4:138399813..138399819
+
Hg19::chr4:151977012..151977014,-p@chr4:151977012..151977014
-
Hg19::chr4:155378912..155378919,+p@chr4:155378912..155378919
+
Hg19::chr4:37563274..37563279,-p@chr4:37563274..37563279
-
Hg19::chr4:4661645..4661651,-p@chr4:4661645..4661651
-
Hg19::chr4:6592942..6592947,-p@chr4:6592942..6592947
-
Hg19::chr4:787481..787486,+p@chr4:787481..787486
+
Hg19::chr4:99534450..99534465,-p@chr4:99534450..99534465
-
Hg19::chr5:132002122..132002127,+p@chr5:132002122..132002127
+
Hg19::chr5:141031076..141031082,-p4@FCHSD1
Hg19::chr5:174972159..174972164,+p@chr5:174972159..174972164
+
Hg19::chr5:176038782..176038807,+p@chr5:176038782..176038807
+
Hg19::chr5:54614660..54614666,-p@chr5:54614660..54614666
-
Hg19::chr5:91793945..91793990,-p@chr5:91793945..91793990
-
Hg19::chr6:14640833..14640843,+p@chr6:14640833..14640843
+
Hg19::chr6:147208136..147208142,-p@chr6:147208136..147208142
-
Hg19::chr6:147769856..147769862,+p@chr6:147769856..147769862
+
Hg19::chr6:16267976..16267985,-p@chr6:16267976..16267985
-
Hg19::chr6:27286882..27286887,+p@chr6:27286882..27286887
+
Hg19::chr6:27760588..27760611,-p@chr6:27760588..27760611
-
Hg19::chr6:28188420..28188425,+p@chr6:28188420..28188425
+
Hg19::chr6:28688272..28688277,+p@chr6:28688272..28688277
+
Hg19::chr6:3209188..3209193,-p@chr6:3209188..3209193
-
Hg19::chr6:43727334..43727337,+p@chr6:43727334..43727337
+
Hg19::chr6:6873326..6873331,+p@chr6:6873326..6873331
+
Hg19::chr7:130983477..130983481,+p@chr7:130983477..130983481
+
Hg19::chr7:150706223..150706226,+p@chr7:150706223..150706226
+
Hg19::chr7:150759072..150759077,-p@chr7:150759072..150759077
-
Hg19::chr7:65392949..65392957,+p@chr7:65392949..65392957
+
Hg19::chr8:110078877..110078879,+p@chr8:110078877..110078879
+
Hg19::chr8:11208442..11208447,+p@chr8:11208442..11208447
+
Hg19::chr8:40551471..40551475,+p@chr8:40551471..40551475
+
Hg19::chr9:101552135..101552140,+p@chr9:101552135..101552140
+
Hg19::chr9:101552164..101552169,+p@chr9:101552164..101552169
+
Hg19::chr9:104134757..104134761,-p@chr9:104134757..104134761
-
Hg19::chr9:130700476..130700480,+p@chr9:130700476..130700480
+
Hg19::chr9:138852986..138853002,-p3@UBAC1
Hg19::chr9:138853016..138853090,-p2@UBAC1
Hg19::chr9:32940992..32941030,+p@chr9:32940992..32941030
+
Hg19::chr9:75972827..75972836,+p@chr9:75972827..75972836
+
Hg19::chrX:48379794..48379808,-p@chrX:48379794..48379808
-
Hg19::chrX:89713597..89713607,+p@chrX:89713597..89713607
+


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:0035173histone kinase activity0.0211939244083363
GO:0005737cytoplasm0.0353148896437898
GO:0007089traversing start control point of mitotic cell cycle0.0353148896437898
GO:0000307cyclin-dependent protein kinase holoenzyme complex0.0356299415866237
GO:0000902cell morphogenesis0.0356299415866237
GO:0032989cellular structure morphogenesis0.0356299415866237
GO:0000086G2/M transition of mitotic cell cycle0.0356299415866237
GO:0000080G1 phase of mitotic cell cycle0.0356299415866237
GO:0006512ubiquitin cycle0.0356299415866237
GO:0043687post-translational protein modification0.0356299415866237
GO:0051318G1 phase0.0356299415866237
GO:0005344oxygen transporter activity0.0356299415866237
GO:0005833hemoglobin complex0.0356299415866237
GO:0006275regulation of DNA replication0.0356299415866237
GO:0004693cyclin-dependent protein kinase activity0.0356299415866237
GO:0015671oxygen transport0.0356299415866237
GO:0006464protein modification process0.0356299415866237
GO:0015669gas transport0.0356299415866237
GO:0007346regulation of progression through mitotic cell cycle0.0356299415866237
GO:0043412biopolymer modification0.0360107307507381
GO:0051052regulation of DNA metabolic process0.0493129337502005



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
bladder cell6.40e-231
lower urinary tract cell6.40e-231
epithelial cell of large intestine2.59e-122
intestinal epithelial cell8.61e-074
Disease
Ontology termp-valuen
chronic leukemia5.29e-698
myeloid leukemia4.26e-1831
leukemia1.95e-1439
hematologic cancer4.38e-1151
immune system cancer4.38e-1151
cancer2.69e-07235
disease of cellular proliferation3.89e-07239


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)
MA0003.11.8654e-12
MA0004.10.169535
MA0006.10.00543639
MA0007.10.0762028
MA0009.10.376649
MA0014.15.40446e-07
MA0017.10.0579559
MA0019.10.216531
MA0024.10.0207539
MA0025.10.294044
MA0027.11.27892
MA0028.10.0187929
MA0029.10.475192
MA0030.10.73151
MA0031.10.831727
MA0038.10.261105
MA0040.10.783627
MA0041.10.646902
MA0042.11.12255
MA0043.10.165843
MA0046.10.359588
MA0048.10.0018632
MA0050.10.360124
MA0051.10.252453
MA0052.10.496009
MA0055.12.07907e-06
MA0056.10
MA0057.10.00242798
MA0058.10.0868626
MA0059.10.0223831
MA0060.16.48225e-05
MA0061.10.00261561
MA0063.10
MA0066.10.412923
MA0067.10.176604
MA0068.10.0506012
MA0069.10.153655
MA0070.10.336607
MA0071.10.461166
MA0072.10.939235
MA0073.16.38747e-09
MA0074.10.0269157
MA0076.10.0305602
MA0077.10.318484
MA0078.10.168002
MA0081.10.085403
MA0083.11.50945
MA0084.10.296283
MA0087.10.326242
MA0088.10.216382
MA0089.10
MA0090.10.075985
MA0091.10.0992052
MA0092.10.290504
MA0093.10.144442
MA0095.10
MA0098.10
MA0100.10.168136
MA0101.10.0311282
MA0103.10.352491
MA0105.10.000102308
MA0106.10.210138
MA0107.10.0604054
MA0108.20.82084
MA0109.10
MA0111.10.156493
MA0113.10.237841
MA0114.10.017165
MA0115.10.135697
MA0116.10.151742
MA0117.10.198115
MA0119.10.178647
MA0122.10.0617897
MA0124.11.7837
MA0125.10.57839
MA0130.10
MA0131.10.0293974
MA0132.10
MA0133.10
MA0135.10.191619
MA0136.10.1585
MA0139.10.000234935
MA0140.13.68272
MA0141.11.14867
MA0142.17.56536
MA0143.11.44569
MA0144.10.270062
MA0145.10.0451163
MA0146.10.00348388
MA0147.10.0122214
MA0148.11.13898
MA0149.10.0407639
MA0062.20.00432729
MA0035.23.23074
MA0039.23.21795e-05
MA0138.20.310115
MA0002.20.36645
MA0137.20.27844
MA0104.20.00159417
MA0047.24.18765
MA0112.20.0805666
MA0065.20.000422641
MA0150.11.39912
MA0151.10
MA0152.10.316774
MA0153.10.546746
MA0154.10.0451376
MA0155.10.000389769
MA0156.10.0226362
MA0157.10.404569
MA0158.10
MA0159.10.312848
MA0160.10.751182
MA0161.10
MA0162.14.64132e-07
MA0163.18.9052e-09
MA0164.10.639137
MA0080.20.0917517
MA0018.20.109784
MA0099.22.1221
MA0079.20
MA0102.20.322868
MA0258.10.115262
MA0259.10.00729833
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
BCL3#602102.350143047873360.01083762433909430.0399671839106874
BCLAF1#9774304.418907675535076.60443440592223e-128.44260128421189e-10
CEBPB#1051311.680990315650130.00246841383229880.0138683453779899
FOSL1#8061123.241924874805960.0003742953785108480.00371941341924781
GATA1#2623302.76740982526543.16538239521499e-071.58860822668841e-05
GATA2#2624363.121207771482616.40110507421014e-106.1052512588624e-08
GTF2B#29594910.64794331144142.30968522203392e-361.19416443021783e-33
GTF2F1#2962262.253273352351697.81193240696417e-050.00120334868532586
HDAC2#3066201.825254453962760.006599868574186950.0281685195757871
HEY1#23462842.308634881774696.42594888985933e-171.30822548948932e-14
JUNB#3726214.372947522831591.64384562941445e-081.19223328951678e-06
JUND#3727341.617813428732070.002767820916122680.0151646442481868
MAFK#7975122.21230474594530.008590671441150410.0327278447013317
POLR2A#5430931.358592825985723.39871836445388e-050.00067431372960714
POU5F1#546036.84569798881440.009952549610873340.0373360031900144
SMARCA4#659755.332173581900950.002654106130880540.0146484273214096
STAT2#677393.995741093047390.00047766630178210.00435200129912072
TAF7#6879644.977662870170963.42445470951413e-291.31006089892654e-26
TAL1#6886377.517951136498554.97957745754765e-221.39054034783107e-19
TBP#6908892.244235313956321.55179694714623e-173.28738582886421e-15



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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