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Coexpression cluster:C122: Difference between revisions

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|tf_chipseq_enrich=BCL3#602;10:2.35014304787336:0.0108376243390943:0.0399671839106874!BCLAF1#9774;30:4.41890767553507:6.60443440592223e-12:8.44260128421189e-10!CEBPB#1051;31:1.68099031565013:0.0024684138322988:0.0138683453779899!FOSL1#8061;12:3.24192487480596:0.000374295378510848:0.00371941341924781!GATA1#2623;30:2.7674098252654:3.16538239521499e-07:1.58860822668841e-05!GATA2#2624;36:3.12120777148261:6.40110507421014e-10:6.1052512588624e-08!GTF2B#2959;49:10.6479433114414:2.30968522203392e-36:1.19416443021783e-33!GTF2F1#2962;26:2.25327335235169:7.81193240696417e-05:0.00120334868532586!HDAC2#3066;20:1.82525445396276:0.00659986857418695:0.0281685195757871!HEY1#23462;84:2.30863488177469:6.42594888985933e-17:1.30822548948932e-14!JUNB#3726;21:4.37294752283159:1.64384562941445e-08:1.19223328951678e-06!JUND#3727;34:1.61781342873207:0.00276782091612268:0.0151646442481868!MAFK#7975;12:2.2123047459453:0.00859067144115041:0.0327278447013317!POLR2A#5430;93:1.35859282598572:3.39871836445388e-05:0.00067431372960714!POU5F1#5460;3:6.8456979888144:0.00995254961087334:0.0373360031900144!SMARCA4#6597;5:5.33217358190095:0.00265410613088054:0.0146484273214096!STAT2#6773;9:3.99574109304739:0.0004776663017821:0.00435200129912072!TAF7#6879;64:4.97766287017096:3.42445470951413e-29:1.31006089892654e-26!TAL1#6886;37:7.51795113649855:4.97957745754765e-22:1.39054034783107e-19!TBP#6908;89:2.24423531395632:1.55179694714623e-17:3.28738582886421e-15
|tf_chipseq_enrich=BCL3#602;10:2.35014304787336:0.0108376243390943:0.0399671839106874!BCLAF1#9774;30:4.41890767553507:6.60443440592223e-12:8.44260128421189e-10!CEBPB#1051;31:1.68099031565013:0.0024684138322988:0.0138683453779899!FOSL1#8061;12:3.24192487480596:0.000374295378510848:0.00371941341924781!GATA1#2623;30:2.7674098252654:3.16538239521499e-07:1.58860822668841e-05!GATA2#2624;36:3.12120777148261:6.40110507421014e-10:6.1052512588624e-08!GTF2B#2959;49:10.6479433114414:2.30968522203392e-36:1.19416443021783e-33!GTF2F1#2962;26:2.25327335235169:7.81193240696417e-05:0.00120334868532586!HDAC2#3066;20:1.82525445396276:0.00659986857418695:0.0281685195757871!HEY1#23462;84:2.30863488177469:6.42594888985933e-17:1.30822548948932e-14!JUNB#3726;21:4.37294752283159:1.64384562941445e-08:1.19223328951678e-06!JUND#3727;34:1.61781342873207:0.00276782091612268:0.0151646442481868!MAFK#7975;12:2.2123047459453:0.00859067144115041:0.0327278447013317!POLR2A#5430;93:1.35859282598572:3.39871836445388e-05:0.00067431372960714!POU5F1#5460;3:6.8456979888144:0.00995254961087334:0.0373360031900144!SMARCA4#6597;5:5.33217358190095:0.00265410613088054:0.0146484273214096!STAT2#6773;9:3.99574109304739:0.0004776663017821:0.00435200129912072!TAF7#6879;64:4.97766287017096:3.42445470951413e-29:1.31006089892654e-26!TAL1#6886;37:7.51795113649855:4.97957745754765e-22:1.39054034783107e-19!TBP#6908;89:2.24423531395632:1.55179694714623e-17:3.28738582886421e-15
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|tfbs_overrepresentation_for_novel_motifs=0.00698473,0.000183181,0.106599,0.342966,0.530771,0.491147,0.255437,0.108925,0.147011,2.45065e-05,0.00584015,0.762827,0.0184687,0.0628072,0.397992,0.282128,0.070026,1.04839,0.00935757,0.0513295,0.48243,0.500573,0.201706,0.130737,0.414668,0.0560801,0.416508,0.197483,0.00617029,0.0316615,0.0325396,0.429772,0.0120386,0.152693,0.0779173,0.000414594,0.000617107,0.029017,0.318832,0.000737998,0.576256,0.173205,0.113266,0.819592,0.00178724,0.0550076,0.0280134,0.0047961,0.0572955,0.420173,0.0640293,0.0321474,0.325551,0.328654,0.279849,0.134289,1.09741,0.0971957,0.0696451,0.0441729,0.277908,0.0288121,0.204675,0.05707,0.0353928,0.0432504,0.380615,0.91731,0.409147,0.234636,0.0202359,0.313764,5.06545e-05,0.984583,0.000420187,0.00934399,0.059804,0.137509,0.40279,0.531269,0.282154,0.0566013,0.671569,0.484908,0.063023,8.01196e-07,0.000246585,0.00544496,0.0803991,0.423396,0.167377,0.0545059,1.09807,0.791718,0.0287456,0.29108,0.320454,0.128146,0.332076,0.940663,1.18013,0.452437,0.124215,0.36564,0.413668,0.152743,0.169593,0.126483,0.0348602,0.00125876,0.287952,0.29177,0.235369,0.0211711,0.141871,0.238766,3.8601e-06,0.123693,0.0424003,0.428522,0.961439,1.03412,0.662919,0.0971683,0.203579,0.742078,0.24279,0.0240288,0.315139,0.770732,0.201328,0.32402,0.100996,1.24465,0.518468,0.0307538,0.297747,0.0585707,0.151435,0.818204,0.465466,1.92483,1.33659,0.298508,0.0397771,0.0887974,0.59806,0.673557,0.0984505,0.0254092,0.176304,1.23154e-09,0.444921,0.000437573,0.601431,0.254562,0.969572,0.733909,0.121706,1.07303e-05,0.131806,0.414105,0.659616,0.00921471,1.34627,0.463368,0.945096,0.585255,1.94295e-06
}}
}}

Revision as of 13:30, 26 November 2012


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)

{{{tfbs_overrepresentation_jaspar}}}



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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