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Coexpression cluster:C120: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.00115511,MA0004.1;0.728346,MA0006.1;0.495645,MA0007.1;0.034242,MA0009.1;0.368026,MA0014.1;0.00101039,MA0017.1;0.150881,MA0019.1;0.1073,MA0024.1;0.424108,MA0025.1;1.01165,MA0027.1;1.27321,MA0028.1;0.0170908,MA0029.1;0.245887,MA0030.1;1.44527,MA0031.1;0.812908,MA0038.1;0.581813,MA0040.1;0.253473,MA0041.1;0.450517,MA0042.1;0.342154,MA0043.1;1.02324,MA0046.1;0.152383,MA0048.1;0.331239,MA0050.1;0.0776461,MA0051.1;0.066238,MA0052.1;0.48438,MA0055.1;0.425245,MA0056.1;0,MA0057.1;0.0769604,MA0058.1;0.427264,MA0059.1;0.915093,MA0060.1;0.0237808,MA0061.1;3.13954,MA0063.1;0,MA0066.1;0.142844,MA0067.1;1.57553,MA0068.1;0.448852,MA0069.1;0.0379029,MA0070.1;0.140764,MA0071.1;0.444744,MA0072.1;0.321813,MA0073.1;0.000827566,MA0074.1;1.31882,MA0076.1;0.00109755,MA0077.1;0.131705,MA0078.1;0.297447,MA0081.1;0.422316,MA0083.1;1.04759,MA0084.1;0.292251,MA0087.1;0.135571,MA0088.1;0.639193,MA0089.1;0,MA0090.1;0.298797,MA0091.1;0.742236,MA0092.1;0.553264,MA0093.1;0.655839,MA0095.1;0,MA0098.1;0,MA0100.1;0.279769,MA0101.1;4.22576,MA0103.1;0.573843,MA0105.1;1.16083,MA0106.1;0.201972,MA0107.1;3.4863,MA0108.2;2.88331,MA0109.1;0,MA0111.1;0.34342,MA0113.1;0.119725,MA0114.1;0.239059,MA0115.1;0.13288,MA0116.1;1.8914,MA0117.1;0.0519976,MA0119.1;0.627704,MA0122.1;0.473337,MA0124.1;0.734285,MA0125.1;0.268905,MA0130.1;0,MA0131.1;0.0842366,MA0132.1;0,MA0133.1;0,MA0135.1;0.0498844,MA0136.1;0.837204,MA0139.1;0.0296376,MA0140.1;0.0432617,MA0141.1;0.414031,MA0142.1;0.264034,MA0143.1;0.229346,MA0144.1;0.252546,MA0145.1;0.66437,MA0146.1;0.308966,MA0147.1;1.49239,MA0148.1;0.473864,MA0149.1;0.0135829,MA0062.2;0.0581602,MA0035.2;0.173798,MA0039.2;0.647657,MA0138.2;0.299859,MA0002.2;0.536259,MA0137.2;0.263412,MA0104.2;0.76624,MA0047.2;0.484493,MA0112.2;1.0511,MA0065.2;0.621668,MA0150.1;0.541628,MA0151.1;0,MA0152.1;0.185994,MA0153.1;0.536473,MA0154.1;0.650067,MA0155.1;0.0123603,MA0156.1;1.20757,MA0157.1;0.392701,MA0158.1;0,MA0159.1;0.102595,MA0160.1;0.142178,MA0161.1;0,MA0162.1;0.015073,MA0163.1;0.00713627,MA0164.1;0.621004,MA0080.2;2.77932,MA0018.2;0.752,MA0099.2;2.07461,MA0079.2;1.10099e-06,MA0102.2;0.3187,MA0258.1;0.716101,MA0259.1;0.687613,MA0442.1;0
}}
}}

Revision as of 18:25, 22 January 2013


Full id: C120_immature_salivary_tongue_skin_cervical_CD14_CD34



Phase1 CAGE Peaks

Hg19::chr10:103893775..103893800,-p@chr10:103893775..103893800
-
Hg19::chr10:135337169..135337187,-p@chr10:135337169..135337187
-
Hg19::chr10:135337234..135337244,-p@chr10:135337234..135337244
-
Hg19::chr10:135337292..135337307,-p@chr10:135337292..135337307
-
Hg19::chr10:81701830..81701837,-p@chr10:81701830..81701837
-
Hg19::chr10:85954269..85954280,+p4@CDHR1
Hg19::chr10:85954282..85954314,+p1@CDHR1
Hg19::chr10:97592419..97592428,+p@chr10:97592419..97592428
+
Hg19::chr11:108408895..108408924,-p3@EXPH5
Hg19::chr11:113258495..113258506,+p1@ANKK1
Hg19::chr11:12214399..12214404,-p@chr11:12214399..12214404
-
Hg19::chr11:12214548..12214586,+p@chr11:12214548..12214586
+
Hg19::chr11:57543275..57543296,+p@chr11:57543275..57543296
+
Hg19::chr11:62311004..62311025,+p@chr11:62311004..62311025
+
Hg19::chr11:65363259..65363275,-p1@KCNK7
Hg19::chr12:112587704..112587710,+p@chr12:112587704..112587710
+
Hg19::chr12:322653..322665,-p8@SLC6A12
Hg19::chr12:52541319..52541358,+p@chr12:52541319..52541358
+
Hg19::chr12:53045991..53045996,-p1@KRT2
Hg19::chr12:53268328..53268340,+p@chr12:53268328..53268340
+
Hg19::chr13:23490561..23490568,-p1@ENST00000379093
Hg19::chr13:78130718..78130733,+p@chr13:78130718..78130733
+
Hg19::chr13:79979347..79979384,+p@chr13:79979347..79979384
+
Hg19::chr14:104583456..104583460,+p1@MIR203
Hg19::chr14:24017647..24017657,-p15@ZFHX2
Hg19::chr14:50234166..50234170,+p6@KLHDC2
Hg19::chr14:67879076..67879080,+p@chr14:67879076..67879080
+
Hg19::chr14:69192856..69192867,-p@chr14:69192856..69192867
-
Hg19::chr14:69223811..69223817,+p@chr14:69223811..69223817
+
Hg19::chr14:94833955..94833966,+p@chr14:94833955..94833966
+
Hg19::chr15:42313237..42313242,-p@chr15:42313237..42313242
-
Hg19::chr15:42448788..42448849,-p1@PLA2G4F
Hg19::chr15:59949497..59949508,-p3@GTF2A2
Hg19::chr16:10915414..10915421,+p@chr16:10915414..10915421
+
Hg19::chr16:10953616..10953637,+p@chr16:10953616..10953637
+
Hg19::chr16:10970721..10970727,-p@chr16:10970721..10970727
-
Hg19::chr16:1257038..1257050,+p@chr16:1257038..1257050
+
Hg19::chr16:31454377..31454381,+p@chr16:31454377..31454381
+
Hg19::chr16:33722353..33722359,+p@chr16:33722353..33722359
+
Hg19::chr16:34571309..34571314,-p@chr16:34571309..34571314
-
Hg19::chr16:75018508..75018512,+p@chr16:75018508..75018512
+
Hg19::chr16:85894104..85894112,-p@chr16:85894104..85894112
-
Hg19::chr17:10009524..10009534,-p@chr17:10009524..10009534
-
Hg19::chr17:10009535..10009542,-p@chr17:10009535..10009542
-
Hg19::chr17:25874072..25874076,+p@chr17:25874072..25874076
+
Hg19::chr17:29887192..29887207,-p@chr17:29887192..29887207
-
Hg19::chr17:39812242..39812247,+p@chr17:39812242..39812247
+
Hg19::chr17:48546232..48546247,-p1@CHAD
Hg19::chr17:7154246..7154280,+p@chr17:7154246..7154280
+
Hg19::chr17:7183607..7183612,-p@chr17:7183607..7183612
-
Hg19::chr17:7819599..7819609,-p1@ENST00000324348
Hg19::chr17:79874727..79874731,+p@chr17:79874727..79874731
+
Hg19::chr18:13562948..13562955,+p@chr18:13562948..13562955
+
Hg19::chr18:23806437..23806449,+p2@TAF4B
Hg19::chr18:53545728..53545733,+p@chr18:53545728..53545733
+
Hg19::chr18:53548086..53548099,-p@chr18:53548086..53548099
-
Hg19::chr19:10024468..10024484,-p@chr19:10024468..10024484
-
Hg19::chr19:1180737..1180757,+p@chr19:1180737..1180757
+
Hg19::chr19:1180760..1180775,+p@chr19:1180760..1180775
+
Hg19::chr19:1180783..1180800,+p@chr19:1180783..1180800
+
Hg19::chr19:2090131..2090140,-p@chr19:2090131..2090140
-
Hg19::chr19:33783896..33783902,+p@chr19:33783896..33783902
+
Hg19::chr19:35481293..35481296,-p@chr19:35481293..35481296
-
Hg19::chr19:40440897..40440908,-p2@FCGBP
Hg19::chr19:55581103..55581143,-p4@RDH13
Hg19::chr19:6062602..6062619,+p@chr19:6062602..6062619
+
Hg19::chr19:6063658..6063670,-p@chr19:6063658..6063670
-
Hg19::chr19:6063965..6063994,+p@chr19:6063965..6063994
+
Hg19::chr19:9732460..9732472,-p2@ZNF561
Hg19::chr1:1100457..1100470,+p@chr1:1100457..1100470
+
Hg19::chr1:117602977..117602984,+p3@TTF2
Hg19::chr1:11865532..11865537,-p11@MTHFR
Hg19::chr1:152878978..152878994,+p@chr1:152878978..152878994
+
Hg19::chr1:157926828..157926838,+p@chr1:157926828..157926838
+
Hg19::chr1:158224235..158224244,+p10@CD1A
Hg19::chr1:16481684..16481727,+p1@ENST00000424774
Hg19::chr1:183442112..183442126,-p@chr1:183442112..183442126
-
Hg19::chr1:19283116..19283132,-p1@IFFO2
Hg19::chr1:19283143..19283154,-p3@IFFO2
Hg19::chr1:212780312..212780339,+p@chr1:212780312..212780339
+
Hg19::chr1:212780356..212780372,+p@chr1:212780356..212780372
+
Hg19::chr1:27181551..27181558,-p@chr1:27181551..27181558
-
Hg19::chr1:29270212..29270216,-p@chr1:29270212..29270216
-
Hg19::chr1:39571788..39571799,-p@chr1:39571788..39571799
-
Hg19::chr1:42902892..42902896,+p@chr1:42902892..42902896
+
Hg19::chr1:85462278..85462283,+p@chr1:85462278..85462283
+
Hg19::chr20:1762918..1762921,-p@chr20:1762918..1762921
-
Hg19::chr20:19095317..19095322,+p@chr20:19095317..19095322
+
Hg19::chr20:23117745..23117783,+p@chr20:23117745..23117783
+
Hg19::chr20:24933916..24933922,-p@chr20:24933916..24933922
-
Hg19::chr20:43588041..43588075,+p@chr20:43588041..43588075
+
Hg19::chr20:44639343..44639375,+p@chr20:44639343..44639375
+
Hg19::chr20:44639385..44639400,+p@chr20:44639385..44639400
+
Hg19::chr2:122041216..122041223,-p@chr2:122041216..122041223
-
Hg19::chr2:173867941..173867955,+p@chr2:173867941..173867955
+
Hg19::chr2:208368220..208368233,+p@chr2:208368220..208368233
+
Hg19::chr2:216002151..216002158,+p@chr2:216002151..216002158
+
Hg19::chr2:216003243..216003282,-p2@ABCA12
Hg19::chr2:216003447..216003472,+p@chr2:216003447..216003472
+
Hg19::chr2:230990020..230990046,+p1@ENST00000445199
Hg19::chr2:38948032..38948038,-p@chr2:38948032..38948038
-
Hg19::chr2:64587249..64587257,-p@chr2:64587249..64587257
-
Hg19::chr2:64680581..64680593,+p@chr2:64680581..64680593
+
Hg19::chr2:64680611..64680624,+p11@LGALSL
Hg19::chr2:71057780..71057794,-p@chr2:71057780..71057794
-
Hg19::chr2:71057873..71057874,-p@chr2:71057873..71057874
-
Hg19::chr2:71058922..71058927,-p@chr2:71058922..71058927
-
Hg19::chr2:73340735..73340740,-p@chr2:73340735..73340740
-
Hg19::chr3:186252359..186252380,+p@chr3:186252359..186252380
+
Hg19::chr3:52099097..52099134,-p1@C3orf74
Hg19::chr3:71080443..71080455,-p@chr3:71080443..71080455
-
Hg19::chr3:71080630..71080635,+p@chr3:71080630..71080635
+
Hg19::chr4:100484667..100484671,-p8@RG9MTD2
Hg19::chr4:106817137..106817150,-p4@INTS12
Hg19::chr4:108745881..108745897,+p4@SGMS2
Hg19::chr4:159149804..159149824,-p@chr4:159149804..159149824
-
Hg19::chr4:3392220..3392256,+p@chr4:3392220..3392256
+
Hg19::chr5:133773054..133773060,+p@chr5:133773054..133773060
+
Hg19::chr5:159933217..159933221,-p@chr5:159933217..159933221
-
Hg19::chr5:79551098..79551103,+p@chr5:79551098..79551103
+
Hg19::chr6:10413321..10413336,+p@chr6:10413321..10413336
+
Hg19::chr6:10413345..10413356,+p@chr6:10413345..10413356
+
Hg19::chr6:106943050..106943075,+p@chr6:106943050..106943075
+
Hg19::chr6:122532780..122532793,+p1@RNU1-18P
Hg19::chr6:132452229..132452234,+p@chr6:132452229..132452234
+
Hg19::chr6:138137434..138137443,+p@chr6:138137434..138137443
+
Hg19::chr6:32140886..32140902,-p26@AGPAT1
Hg19::chr6:32632755..32632783,-p5@HLA-DQB1
Hg19::chr6:32729494..32729506,-p1@M95729
Hg19::chr6:32729634..32729642,-p2@M95729
Hg19::chr6:36992669..36992691,+p@chr6:36992669..36992691
+
Hg19::chr7:2284179..2284201,+p3@NUDT1
Hg19::chr7:39767535..39767539,+p@chr7:39767535..39767539
+
Hg19::chr7:42928540..42928555,+p@chr7:42928540..42928555
+
Hg19::chr7:55594397..55594400,+p@chr7:55594397..55594400
+
Hg19::chr8:144261054..144261063,-p@chr8:144261054..144261063
-
Hg19::chr8:22069222..22069228,+p@chr8:22069222..22069228
+
Hg19::chr8:57233103..57233123,-p2@SDR16C5
Hg19::chr8:62629856..62629862,+p@chr8:62629856..62629862
+
Hg19::chr8:987779..987786,+p@chr8:987779..987786
+
Hg19::chr9:109626921..109626926,-p@chr9:109626921..109626926
-
Hg19::chr9:111314011..111314037,+p@chr9:111314011..111314037
+
Hg19::chr9:134510706..134510711,-p@chr9:134510706..134510711
-
Hg19::chr9:136004782..136004793,-p23@RALGDS
Hg19::chr9:34662651..34662656,-p1@CCL27
Hg19::chr9:87445344..87445355,+p@chr9:87445344..87445355
+
Hg19::chrX:131156808..131156816,+p6@MST4
Hg19::chrX:135838814..135838818,+p@chrX:135838814..135838818
+
Hg19::chrY:27869488..27869491,+p1@ENST00000516617


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:0016591DNA-directed RNA polymerase II, holoenzyme0.0331363952634676
GO:0044451nucleoplasm part0.0455375014718003
GO:0006644phospholipid metabolic process0.0455375014718003
GO:0005654nucleoplasm0.0455375014718003
GO:0032980keratinocyte activation0.0455375014718003
GO:0003717RNA polymerase II transcription termination factor activity0.0455375014718003
GO:0006643membrane lipid metabolic process0.0481807030480791
GO:00084138-oxo-7,8-dihydroguanine triphosphatase activity0.0481807030480791
GO:0033188sphingomyelin synthase activity0.0481807030480791
GO:0047493ceramide cholinephosphotransferase activity0.0481807030480791
GO:0031981nuclear lumen0.0481807030480791
GO:0006352transcription initiation0.0481807030480791
GO:0008654phospholipid biosynthetic process0.0481807030480791
GO:0004489methylenetetrahydrofolate reductase (NADPH) activity0.0481807030480791
GO:0006654phosphatidic acid biosynthetic process0.0481807030480791
GO:0051546keratinocyte migration0.0481807030480791
GO:0006686sphingomyelin biosynthetic process0.0481807030480791



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><br>

Uber Anatomy
Ontology termp-valuen
tonsil4.66e-661
mucosa-associated lymphoid tissue4.66e-661
lymphoid tissue4.66e-661
tonsillar ring4.66e-661
lymphoid system6.56e-0810
chordate pharynx6.56e-0810
pharyngeal region of foregut6.56e-0810
immune system2.32e-0793
pharynx2.63e-0711


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)
MA0003.10.00115511
MA0004.10.728346
MA0006.10.495645
MA0007.10.034242
MA0009.10.368026
MA0014.10.00101039
MA0017.10.150881
MA0019.10.1073
MA0024.10.424108
MA0025.11.01165
MA0027.11.27321
MA0028.10.0170908
MA0029.10.245887
MA0030.11.44527
MA0031.10.812908
MA0038.10.581813
MA0040.10.253473
MA0041.10.450517
MA0042.10.342154
MA0043.11.02324
MA0046.10.152383
MA0048.10.331239
MA0050.10.0776461
MA0051.10.066238
MA0052.10.48438
MA0055.10.425245
MA0056.10
MA0057.10.0769604
MA0058.10.427264
MA0059.10.915093
MA0060.10.0237808
MA0061.13.13954
MA0063.10
MA0066.10.142844
MA0067.11.57553
MA0068.10.448852
MA0069.10.0379029
MA0070.10.140764
MA0071.10.444744
MA0072.10.321813
MA0073.10.000827566
MA0074.11.31882
MA0076.10.00109755
MA0077.10.131705
MA0078.10.297447
MA0081.10.422316
MA0083.11.04759
MA0084.10.292251
MA0087.10.135571
MA0088.10.639193
MA0089.10
MA0090.10.298797
MA0091.10.742236
MA0092.10.553264
MA0093.10.655839
MA0095.10
MA0098.10
MA0100.10.279769
MA0101.14.22576
MA0103.10.573843
MA0105.11.16083
MA0106.10.201972
MA0107.13.4863
MA0108.22.88331
MA0109.10
MA0111.10.34342
MA0113.10.119725
MA0114.10.239059
MA0115.10.13288
MA0116.11.8914
MA0117.10.0519976
MA0119.10.627704
MA0122.10.473337
MA0124.10.734285
MA0125.10.268905
MA0130.10
MA0131.10.0842366
MA0132.10
MA0133.10
MA0135.10.0498844
MA0136.10.837204
MA0139.10.0296376
MA0140.10.0432617
MA0141.10.414031
MA0142.10.264034
MA0143.10.229346
MA0144.10.252546
MA0145.10.66437
MA0146.10.308966
MA0147.11.49239
MA0148.10.473864
MA0149.10.0135829
MA0062.20.0581602
MA0035.20.173798
MA0039.20.647657
MA0138.20.299859
MA0002.20.536259
MA0137.20.263412
MA0104.20.76624
MA0047.20.484493
MA0112.21.0511
MA0065.20.621668
MA0150.10.541628
MA0151.10
MA0152.10.185994
MA0153.10.536473
MA0154.10.650067
MA0155.10.0123603
MA0156.11.20757
MA0157.10.392701
MA0158.10
MA0159.10.102595
MA0160.10.142178
MA0161.10
MA0162.10.015073
MA0163.10.00713627
MA0164.10.621004
MA0080.22.77932
MA0018.20.752
MA0099.22.07461
MA0079.21.10099e-06
MA0102.20.3187
MA0258.10.716101
MA0259.10.687613
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
GATA3#2625122.193544941519950.009168760899619630.0346822245416651



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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