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Coexpression cluster:C132: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.348493,0.000524304,0.0470045,1.3085,0.508258,1.59606,0.08963,0.159782,0.368514,0.329958,0.117197,0.0568017,0.21318,0.0801058,0.81344,1.21491,0.0185446,0.578823,0.153443,0.205298,0.445049,0.118984,0.148609,0.480659,0.159258,0.699011,0.465019,0.0118314,0.044923,0.508764,0.0184673,0.482224,0.0047007,0.223949,0.00947215,0.250014,0.0366791,0.0392333,0.160537,0.201487,0.330235,0.134298,0.2404,0.183126,0.164084,0.132209,0.477213,0.788175,1.69065,0.0800851,0.079261,0.197702,0.253802,0.160888,0.308375,0.165609,1.29733,0.0221285,0.154788,0.121628,0.133308,0.0377082,0.212612,0.17976,0.109169,0.764459,0.413386,0.96213,0.243778,0.252079,0.0618718,0.42045,0.186811,0.0916197,0.00227447,0.191346,0.473805,0.161894,0.0967743,0.0860272,1.01376,0.178594,0.210791,0.00398582,0.0719582,0.00238101,0.0312233,2.55884,0.589681,0.445018,1.62713,0.0627025,0.116321,2.04295,0.0216297,0.144528,0.437705,0.147139,0.384434,0.015812,0.68408,0.809907,0.142875,1.00296,0.0482968,0.00180454,0.0766872,0.622874,0.0489916,0.0961489,0.166243,0.936211,0.132947,0.221235,0.155742,0.54703,0.00641996,0.0441154,0.142219,0.245043,1.53488,0.0961584,0.0830188,0.382538,0.627374,0.162675,0.656632,0.119726,0.345282,0.00901604,0.843245,1.20793,5.44721,0.374219,0.189873,0.255662,0.244319,0.377896,0.165755,4.67519,0.487708,0.877572,0.295406,1.36182,0.731289,0.112995,0.0082406,0.697949,0.212466,0.040758,0.072025,0.000456878,0.225938,0.0568376,0.0375078,0.272597,0.339548,0.00666376,0.159369,0.0308898,0.145179,0.795423,0.451993,0.708369,1.894,0.209506,0.123963,1.87163,0.000366411
|tfbs_overrepresentation_jaspar=MA0003.1;2.04215e-10,MA0004.1;0.0276601,MA0006.1;0.020479,MA0007.1;0.414025,MA0009.1;1.12902,MA0014.1;1.15216e-07,MA0017.1;0.427217,MA0019.1;0.0596055,MA0024.1;0.0251638,MA0025.1;2.87425,MA0027.1;1.30565,MA0028.1;0.0961311,MA0029.1;0.843858,MA0030.1;0.504839,MA0031.1;0.190659,MA0038.1;0.182207,MA0040.1;0.124032,MA0041.1;0.555535,MA0042.1;0.185866,MA0043.1;2.11219,MA0046.1;0.400287,MA0048.1;0.0133716,MA0050.1;0.107781,MA0051.1;0.921498,MA0052.1;0.126786,MA0055.1;0.00302427,MA0056.1;0,MA0057.1;0.187695,MA0058.1;0.00513614,MA0059.1;0.900754,MA0060.1;2.26687,MA0061.1;0.032579,MA0063.1;0,MA0066.1;0.483872,MA0067.1;0.192002,MA0068.1;0.037571,MA0069.1;0.698092,MA0070.1;0.0429203,MA0071.1;0.753582,MA0072.1;1.4551,MA0073.1;7.52336e-10,MA0074.1;0.174739,MA0076.1;0.470771,MA0077.1;1.90355,MA0078.1;1.12782,MA0081.1;1.90163,MA0083.1;1.6238,MA0084.1;0.315416,MA0087.1;0.159565,MA0088.1;0.0490992,MA0089.1;0,MA0090.1;0.101937,MA0091.1;0.492548,MA0092.1;0.684299,MA0093.1;0.00361484,MA0095.1;0,MA0098.1;0,MA0100.1;0.104785,MA0101.1;0.292599,MA0103.1;0.0339817,MA0105.1;0.00474102,MA0106.1;0.132942,MA0107.1;0.198183,MA0108.2;0.366618,MA0109.1;0,MA0111.1;0.601307,MA0113.1;0.458142,MA0114.1;0.445892,MA0115.1;0.892203,MA0116.1;0.210075,MA0117.1;0.222158,MA0119.1;0.151386,MA0122.1;0.247735,MA0124.1;0.128191,MA0125.1;1.05115,MA0130.1;0,MA0131.1;0.0369142,MA0132.1;0,MA0133.1;0,MA0135.1;0.814474,MA0136.1;1.96421,MA0139.1;0.0562653,MA0140.1;1.57206,MA0141.1;0.031712,MA0142.1;0.531882,MA0143.1;0.458631,MA0144.1;0.0930138,MA0145.1;0.0853891,MA0146.1;0.0294449,MA0147.1;0.222475,MA0148.1;0.0858313,MA0149.1;0.20648,MA0062.2;1.24065,MA0035.2;0.981141,MA0039.2;3.67744e-05,MA0138.2;0.0315277,MA0002.2;0.733851,MA0137.2;0.25166,MA0104.2;0.104143,MA0047.2;0.015443,MA0112.2;0.0322927,MA0065.2;0.310692,MA0150.1;0.0496088,MA0151.1;0,MA0152.1;0.771905,MA0153.1;1.00269,MA0154.1;0.00404551,MA0155.1;0.00996293,MA0156.1;1.22679,MA0157.1;0.129959,MA0158.1;0,MA0159.1;0.0206153,MA0160.1;0.304606,MA0161.1;0,MA0162.1;0.000548696,MA0163.1;9.45204e-06,MA0164.1;0.305983,MA0080.2;1.71455,MA0018.2;0.0581942,MA0099.2;0.238217,MA0079.2;4.03012e-12,MA0102.2;2.45926,MA0258.1;0.782835,MA0259.1;0.0769413,MA0442.1;0
}}
}}

Revision as of 18:27, 22 January 2013


Full id: C132_acute_small_Dendritic_Macrophage_CD14_Neutrophils_Monocytederived



Phase1 CAGE Peaks

Hg19::chr10:134258472..134258491,-p@chr10:134258472..134258491
-
Hg19::chr10:134258649..134258668,+p1@C10orf91
Hg19::chr10:38446333..38446347,-p@chr10:38446333..38446347
-
Hg19::chr10:38446358..38446374,-p@chr10:38446358..38446374
-
Hg19::chr10:65225034..65225046,+p3@LOC84989
Hg19::chr10:65280689..65280700,+p29@REEP3
Hg19::chr10:65280796..65280817,+p13@REEP3
Hg19::chr10:65288352..65288355,+p@chr10:65288352..65288355
+
Hg19::chr10:90251152..90251159,-p@chr10:90251152..90251159
-
Hg19::chr11:59949916..59949949,-p11@MS4A6A
Hg19::chr11:59951230..59951237,-p15@MS4A6A
Hg19::chr11:59951430..59951444,-p9@MS4A6A
Hg19::chr11:59951889..59951902,-p6@MS4A6A
Hg19::chr11:94308189..94308199,+p@chr11:94308189..94308199
+
Hg19::chr12:117099342..117099357,+p1@ENST00000546835
Hg19::chr12:24737089..24737109,-p1@LINC00477
Hg19::chr13:32575640..32575659,+p@chr13:32575640..32575659
+
Hg19::chr13:46742704..46742715,-p25@LCP1
Hg19::chr14:21387491..21387506,+p2@RNASE2
Hg19::chr15:50406680..50406709,-p7@ATP8B4
Hg19::chr15:75299835..75299854,+p@chr15:75299835..75299854
+
Hg19::chr16:54304608..54304618,-p2@ENST00000561336
Hg19::chr16:54304718..54304733,-p1@ENST00000561336
Hg19::chr16:54304905..54304937,+p@chr16:54304905..54304937
+
Hg19::chr17:73266490..73266504,-p11@MIF4GD
Hg19::chr18:22804637..22804660,-p10@ZNF521
Hg19::chr18:22805268..22805280,-p8@ZNF521
Hg19::chr18:61568727..61568742,+p@chr18:61568727..61568742
+
Hg19::chr19:16250693..16250727,-p1@uc002ndq.1
Hg19::chr19:51226648..51226668,+p3@CLEC11A
Hg19::chr1:105010966..105010975,-p@chr1:105010966..105010975
-
Hg19::chr1:105011001..105011012,-p@chr1:105011001..105011012
-
Hg19::chr1:155151392..155151434,-p@chr1:155151392..155151434
-
Hg19::chr1:156460402..156460417,-p22@MEF2D
Hg19::chr1:156460436..156460462,-p7@MEF2D
Hg19::chr1:156460473..156460486,-p12@MEF2D
Hg19::chr1:159907468..159907492,+p@chr1:159907468..159907492
+
Hg19::chr1:173640099..173640102,-p@chr1:173640099..173640102
-
Hg19::chr1:173640358..173640371,+p@chr1:173640358..173640371
+
Hg19::chr1:188783243..188783249,+p@chr1:188783243..188783249
+
Hg19::chr1:189110597..189110603,-p@chr1:189110597..189110603
-
Hg19::chr1:189110612..189110619,-p@chr1:189110612..189110619
-
Hg19::chr1:189110647..189110655,-p@chr1:189110647..189110655
-
Hg19::chr1:189118891..189118896,+p@chr1:189118891..189118896
+
Hg19::chr1:189279755..189279759,+p@chr1:189279755..189279759
+
Hg19::chr1:21012873..21012898,-p10@KIF17
Hg19::chr1:243635289..243635294,+p@chr1:243635289..243635294
+
Hg19::chr1:246269797..246269820,-p@chr1:246269797..246269820
-
Hg19::chr1:246271419..246271436,-p@chr1:246271419..246271436
-
Hg19::chr1:40254482..40254550,-p1@BMP8B
Hg19::chr1:40265085..40265119,+p@chr1:40265085..40265119
+
Hg19::chr1:40562908..40562931,-p1@PPT1
Hg19::chr1:40723846..40723871,+p2@ZMPSTE24
Hg19::chr1:40723874..40723943,+p1@ZMPSTE24
Hg19::chr1:40778264..40778280,-p@chr1:40778264..40778280
-
Hg19::chr1:40778285..40778317,-p@chr1:40778285..40778317
-
Hg19::chr1:40942922..40942997,+p1@ZNF642
Hg19::chr1:40974395..40974430,+p2@DEM1
Hg19::chr1:40974431..40974446,+p1@DEM1
Hg19::chr1:40974453..40974466,+p3@DEM1
Hg19::chr1:40997285..40997352,+p1@ZNF684
Hg19::chr1:40997363..40997392,+p2@ZNF684
Hg19::chr1:41157363..41157416,+p1@NFYC
Hg19::chr1:41157421..41157482,+p2@NFYC
Hg19::chr1:41327085..41327095,-p@chr1:41327085..41327095
-
Hg19::chr1:44172999..44173025,-p2@LOC100132774
Hg19::chr1:44265188..44265223,-p@chr1:44265188..44265223
-
Hg19::chr1:44267074..44267083,+p@chr1:44267074..44267083
+
Hg19::chr1:44303803..44303811,+p@chr1:44303803..44303811
+
Hg19::chr1:44303822..44303850,+p@chr1:44303822..44303850
+
Hg19::chr1:44303858..44303865,+p@chr1:44303858..44303865
+
Hg19::chr1:82286670..82286676,+p@chr1:82286670..82286676
+
Hg19::chr20:32810271..32810284,+p@chr20:32810271..32810284
+
Hg19::chr20:44538665..44538730,-p4@PLTP
Hg19::chr21:15680790..15680806,+p@chr21:15680790..15680806
+
Hg19::chr2:121130183..121130188,+p@chr2:121130183..121130188
+
Hg19::chr2:169939659..169939666,+p@chr2:169939659..169939666
+
Hg19::chr2:169939683..169939692,+p@chr2:169939683..169939692
+
Hg19::chr2:169939710..169939721,+p@chr2:169939710..169939721
+
Hg19::chr2:169939733..169939745,+p@chr2:169939733..169939745
+
Hg19::chr2:169939776..169939787,+p@chr2:169939776..169939787
+
Hg19::chr2:169939816..169939834,+p@chr2:169939816..169939834
+
Hg19::chr2:169939851..169939861,+p@chr2:169939851..169939861
+
Hg19::chr2:169939862..169939872,+p@chr2:169939862..169939872
+
Hg19::chr2:169939880..169939894,+p@chr2:169939880..169939894
+
Hg19::chr2:63282550..63282565,+p@chr2:63282550..63282565
+
Hg19::chr3:125053819..125053839,-p@chr3:125053819..125053839
-
Hg19::chr3:18462463..18462475,-p45@SATB1
Hg19::chr3:26584176..26584198,+p@chr3:26584176..26584198
+
Hg19::chr3:4562205..4562207,+p@chr3:4562205..4562207
+
Hg19::chr4:180738607..180738609,-p@chr4:180738607..180738609
-
Hg19::chr4:180973985..180973992,+p@chr4:180973985..180973992
+
Hg19::chr4:180980059..180980067,+p@chr4:180980059..180980067
+
Hg19::chr4:180980085..180980101,+p@chr4:180980085..180980101
+
Hg19::chr4:181092976..181092979,+p@chr4:181092976..181092979
+
Hg19::chr4:48198802..48198830,-p@chr4:48198802..48198830
-
Hg19::chr4:48493343..48493374,-p@chr4:48493343..48493374
-
Hg19::chr4:62065829..62065850,+p@chr4:62065829..62065850
+
Hg19::chr5:113697844..113697858,+p2@KCNN2
Hg19::chr5:113743752..113743764,+p@chr5:113743752..113743764
+
Hg19::chr5:113743792..113743800,+p@chr5:113743792..113743800
+
Hg19::chr5:113743823..113743833,+p@chr5:113743823..113743833
+
Hg19::chr5:113769205..113769213,+p9@KCNN2
Hg19::chr5:176889489..176889507,-p20@DBN1
Hg19::chr5:32388629..32388636,-p14@ZFR
Hg19::chr5:32388639..32388655,-p8@ZFR
Hg19::chr5:32388671..32388686,-p10@ZFR
Hg19::chr5:32388687..32388699,-p9@ZFR
Hg19::chr5:32388710..32388733,-p5@ZFR
Hg19::chr5:49739173..49739184,-p8@EMB
Hg19::chr5:59544794..59544804,-p@chr5:59544794..59544804
-
Hg19::chr5:59544814..59544835,-p@chr5:59544814..59544835
-
Hg19::chr5:59544841..59544865,-p@chr5:59544841..59544865
-
Hg19::chr5:72152728..72152735,+p@chr5:72152728..72152735
+
Hg19::chr6:135516909..135516925,+p6@MYB
Hg19::chr6:147092283..147092294,-p@chr6:147092283..147092294
-
Hg19::chr6:170108056..170108066,-p8@PHF10
Hg19::chr6:170451118..170451126,+p@chr6:170451118..170451126
+
Hg19::chr6:170478046..170478060,-p@chr6:170478046..170478060
-
Hg19::chr6:170478075..170478104,-p@chr6:170478075..170478104
-
Hg19::chr6:38670845..38670895,-p2@GLO1
Hg19::chr6:76330342..76330351,+p23@SENP6
Hg19::chr6:76330355..76330365,+p20@SENP6
Hg19::chr6:79728851..79728869,-p@chr6:79728851..79728869
-
Hg19::chr6:79729013..79729033,-p@chr6:79729013..79729033
-
Hg19::chr6:79729149..79729164,-p@chr6:79729149..79729164
-
Hg19::chr6:79787873..79787890,-p3@PHIP
Hg19::chr7:11676716..11676733,-p7@THSD7A
Hg19::chr7:11676734..11676740,-p26@THSD7A
Hg19::chr8:58333441..58333449,+p@chr8:58333441..58333449
+
Hg19::chr8:58375259..58375264,+p@chr8:58375259..58375264
+
Hg19::chr8:58375450..58375469,+p@chr8:58375450..58375469
+
Hg19::chr8:58375548..58375550,+p@chr8:58375548..58375550
+
Hg19::chr9:108126806..108126826,+p@chr9:108126806..108126826
+
Hg19::chr9:211250..211266,+p@chr9:211250..211266
+
Hg19::chrX:108780604..108780616,+p@chrX:108780604..108780616
+
Hg19::chrX:113302230..113302241,-p@chrX:113302230..113302241
-
Hg19::chrX:153524141..153524157,+p1@TKTL1


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:0050803regulation of synapse structure and activity0.0447249954149928



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><br>disease_data<br>

Disease
Ontology termp-valuen
myeloid leukemia1.29e-4431
leukemia1.45e-3539
hematologic cancer2.68e-2751
immune system cancer2.68e-2751
organ system cancer2.97e-10137


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)
MA0003.12.04215e-10
MA0004.10.0276601
MA0006.10.020479
MA0007.10.414025
MA0009.11.12902
MA0014.11.15216e-07
MA0017.10.427217
MA0019.10.0596055
MA0024.10.0251638
MA0025.12.87425
MA0027.11.30565
MA0028.10.0961311
MA0029.10.843858
MA0030.10.504839
MA0031.10.190659
MA0038.10.182207
MA0040.10.124032
MA0041.10.555535
MA0042.10.185866
MA0043.12.11219
MA0046.10.400287
MA0048.10.0133716
MA0050.10.107781
MA0051.10.921498
MA0052.10.126786
MA0055.10.00302427
MA0056.10
MA0057.10.187695
MA0058.10.00513614
MA0059.10.900754
MA0060.12.26687
MA0061.10.032579
MA0063.10
MA0066.10.483872
MA0067.10.192002
MA0068.10.037571
MA0069.10.698092
MA0070.10.0429203
MA0071.10.753582
MA0072.11.4551
MA0073.17.52336e-10
MA0074.10.174739
MA0076.10.470771
MA0077.11.90355
MA0078.11.12782
MA0081.11.90163
MA0083.11.6238
MA0084.10.315416
MA0087.10.159565
MA0088.10.0490992
MA0089.10
MA0090.10.101937
MA0091.10.492548
MA0092.10.684299
MA0093.10.00361484
MA0095.10
MA0098.10
MA0100.10.104785
MA0101.10.292599
MA0103.10.0339817
MA0105.10.00474102
MA0106.10.132942
MA0107.10.198183
MA0108.20.366618
MA0109.10
MA0111.10.601307
MA0113.10.458142
MA0114.10.445892
MA0115.10.892203
MA0116.10.210075
MA0117.10.222158
MA0119.10.151386
MA0122.10.247735
MA0124.10.128191
MA0125.11.05115
MA0130.10
MA0131.10.0369142
MA0132.10
MA0133.10
MA0135.10.814474
MA0136.11.96421
MA0139.10.0562653
MA0140.11.57206
MA0141.10.031712
MA0142.10.531882
MA0143.10.458631
MA0144.10.0930138
MA0145.10.0853891
MA0146.10.0294449
MA0147.10.222475
MA0148.10.0858313
MA0149.10.20648
MA0062.21.24065
MA0035.20.981141
MA0039.23.67744e-05
MA0138.20.0315277
MA0002.20.733851
MA0137.20.25166
MA0104.20.104143
MA0047.20.015443
MA0112.20.0322927
MA0065.20.310692
MA0150.10.0496088
MA0151.10
MA0152.10.771905
MA0153.11.00269
MA0154.10.00404551
MA0155.10.00996293
MA0156.11.22679
MA0157.10.129959
MA0158.10
MA0159.10.0206153
MA0160.10.304606
MA0161.10
MA0162.10.000548696
MA0163.19.45204e-06
MA0164.10.305983
MA0080.21.71455
MA0018.20.0581942
MA0099.20.238217
MA0079.24.03012e-12
MA0102.22.45926
MA0258.10.782835
MA0259.10.0769413
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
BATF#10538122.118069721069880.01171708662272550.0427724854872711
MEF2A#4205152.037307707570010.007066668575740780.0294742731382504
SETDB1#9869144.090437438348899.71341096030917e-060.000254953236311568
SPI1#6688352.080806686944171.71472541810345e-050.00039221245716449



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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