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Coexpression cluster:C186: Difference between revisions

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{{Coexpression_clusters
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pit development!0.00603402598852654!220$GO:0002072!optic cup morphogenesis involved in camera-type eye development!0.00603402598852654!220$GO:0021768!nucleus accumbens development!0.00603402598852654!220$GO:0043584!nose development!0.00603402598852654!220$GO:0021756!striatum development!0.00603402598852654!220$GO:0048857!neural nucleus development!0.00603402598852654!220$GO:0021544!subpallium development!0.00775757666933773!220$GO:0048048!embryonic eye morphogenesis!0.00904997327703826!220$GO:0042573!retinoic acid metabolic process!0.0100549338569124!220$GO:0004028!3-chloroallyl aldehyde dehydrogenase activity!0.0108586892361296!220$GO:0021761!limbic system development!0.0115161135774329!220$GO:0048562!embryonic organ morphogenesis!0.0150779615211111!220$GO:0021537!telencephalon development!0.0153090288070116!220$GO:0048593!camera-type eye morphogenesis!0.0167981898572595!220$GO:0004030!aldehyde dehydrogenase [NAD(P)+] activity!0.016883340376704!220$GO:0006776!vitamin A metabolic process!0.0169577140091317!220$GO:0006775!fat-soluble vitamin metabolic process!0.0191488592113784!220$GO:0048568!embryonic organ development!0.0200921158836862!220$GO:0016331!morphogenesis of embryonic epithelium!0.0209356343747139!220$GO:0048592!eye morphogenesis!0.0234994728631865!220$GO:0043010!camera-type eye development!0.0292529612633874!220$GO:0030286!dynein complex!0.0339912580765414!8632$GO:0030900!forebrain development!0.0339912580765414!220$GO:0001654!eye development!0.0339912580765414!220$GO:0044430!cytoskeletal part!0.0339912580765414!84176;8632$GO:0016620!oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor!0.0347134486806925!220$GO:0002009!morphogenesis of an epithelium!0.0420867596980804!220$GO:0016903!oxidoreductase activity, acting on the aldehyde or oxo group of 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73807,0.983771,0.950856,0.917771,0.999609,0.973405,0.954536,0.936407,0.997082,0.978993,0.89878,0.920886,0.895874,0.99933,0.633675,0.94886,0.981642,0.994739,0.999419,0.998694,0.971935,0.807504|tfbs_overrepresentation_for_novel_motifs=0.0908346,0.0281099,0.00321429,0.170845,0.397715,0.308705,0.051054,1.24815,0.0755212,0.000231795,0.0565685,0.186781,0.0282389,0.128825,0.95607,0.484939,0.0557381,3.84974,0.0202106,0.280821,0.570011,0.279047,0.158552,0.157468,0.387837,0.0189107,1.05042,0.0690829,0.409468,1.02358,0.351278,0.240432,0.21272,0.138345,0.107138,0.00115351,0.00955375,0.311157,1.68252,0.00198657,0.396737,0.0106747,0.0725605,0.945405,0.00551053,0.00549789,0.141088,0.380156,0.142675,0.276943,0.0932044,0.0567949,0.457181,0.324276,0.175541,0.00937407,3.33859,0.21812,0.570513,0.216591,0.0834526,0.0525581,0.277329,0.179119,0.0608111,0.624532,0.229345,0.506058,0.229976,0.375511,0.00885633,0.717041,0.000599584,0.174395,0.0249571,0.0326291,0.153509,0.164528,0.846512,0.756778,0.359258,1.09193,0.545569,0.408455,0.146106,6.08143e-09,0.000458542,0.0153313,0.110143,0.590911,0.292382,0.132198,0.931331,0.1532,0.00635647,0.396126,0.876226,1.05438,0.273634,0.0500368,0.0163208,0.915378,0.298015,0.207848,0.14095,0.0165331,0.0519719,0.450734,0.0666638,0.00453345,0.289683,1.02989,0.147155,0.142351,0.718782,0.262967,5.4833e-05,0.0442178,0.343011,0.244024,0.506554,0.492907,0.165027,0.0662005,0.337769,0.165171,0.133768,0.263079,0.566786,1.12092,0.132546,2.47778,1.1111,0.338243,0.301524,0.0120697,0.101411,0.156509,0.271796,1.00864,0.63687,0.689628,1.03881,0.623861,0.142322,0.0953854,0.0318406,0.858349,0.921867,0.00325055,0.0720824,1.55602e-09,0.414233,0.0353183,0.142975,0.399261,0.0994245,0.666499,0.13805,0.000568413,0.245817,1.27366,0.489907,1.14777,1.42096,0.160952,0.0708663,0.283263,6.34701e-06|tfbs_overrepresentation_jaspar=MA0003.1;4.99104e-09,MA0004.1;1.18494,MA0006.1;0.0457519,MA0007.1;0.0490025,MA0009.1;0.112474,MA0014.1;1.8067e-07,MA0017.1;0.0353272,MA0019.1;0.192717,MA0024.1;0.068993,MA0025.1;1.63168,MA0027.1;1.47809,MA0028.1;0.0247631,MA0029.1;0.263395,MA0030.1;0.53603,MA0031.1;0.736736,MA0038.1;1.43522,MA0040.1;0.569275,MA0041.1;0.295713,MA0042.1;0.825469,MA0043.1;0.732147,MA0046.1;0.348554,MA0048.1;0.00208597,MA0050.1;0.122838,MA0051.1;0.0504177,MA0052.1;0.0799011,MA0055.1;0.0025854,MA0056.1;0,MA0057.1;0.00359348,MA0058.1;2.12212,MA0059.1;1.14824,MA0060.1;0.825403,MA0061.1;0.748833,MA0063.1;0,MA0066.1;1.43766,MA0067.1;0.304116,MA0068.1;0.0140086,MA0069.1;0.105679,MA0070.1;0.330546,MA0071.1;0.0368616,MA0072.1;0.0986844,MA0073.1;2.93657e-06,MA0074.1;0.0500929,MA0076.1;0.00615153,MA0077.1;0.316229,MA0078.1;0.481625,MA0081.1;0.314544,MA0083.1;1.2248,MA0084.1;0.448027,MA0087.1;0.32237,MA0088.1;0.787964,MA0089.1;0,MA0090.1;0.595868,MA0091.1;0.0612406,MA0092.1;0.09894,MA0093.1;2.12441,MA0095.1;0,MA0098.1;0,MA0100.1;0.315613,MA0101.1;0.100637,MA0103.1;0.68197,MA0105.1;0.141072,MA0106.1;6.29814,MA0107.1;0.382797,MA0108.2;0.0493529,MA0109.1;0,MA0111.1;0.892901,MA0113.1;0.4014,MA0114.1;0.0558823,MA0115.1;0.251028,MA0116.1;0.032712,MA0117.1;0.409173,MA0119.1;0.587735,MA0122.1;0.443081,MA0124.1;0.636439,MA0125.1;0.51417,MA0130.1;0,MA0131.1;0.0282896,MA0132.1;0,MA0133.1;0,MA0135.1;0.127133,MA0136.1;0.0554464,MA0139.1;0.0153393,MA0140.1;0.614017,MA0141.1;0.000585776,MA0142.1;0.654658,MA0143.1;0.660354,MA0144.1;0.132301,MA0145.1;0.197284,MA0146.1;0.00438042,MA0147.1;0.292742,MA0148.1;1.33601,MA0149.1;0.00598841,MA0062.2;0.00865138,MA0035.2;0.389976,MA0039.2;7.04958e-06,MA0138.2;0.258548,MA0002.2;0.156629,MA0137.2;0.330221,MA0104.2;0.188886,MA0047.2;1.21119,MA0112.2;0.0387444,MA0065.2;0.0136882,MA0150.1;3.22736,MA0151.1;0,MA0152.1;0.407566,MA0153.1;0.490722,MA0154.1;0.023977,MA0155.1;0.0183044,MA0156.1;0.126828,MA0157.1;0.322729,MA0158.1;0,MA0159.1;0.0698723,MA0160.1;0.190068,MA0161.1;0,MA0162.1;8.89507e-06,MA0163.1;3.45651e-08,MA0164.1;0.223694,MA0080.2;0.0964526,MA0018.2;0.18974,MA0099.2;5.18072,MA0079.2;0,MA0102.2;0.478533,MA0258.1;0.112859,MA0259.1;0.0409197,MA0442.1;0}}
|full_id=C186_squamous_papillotubular_large_Tracheal_oral_Small_epidermoid
|id=C186
}}

Latest revision as of 10:51, 17 September 2013


Full id: C186_squamous_papillotubular_large_Tracheal_oral_Small_epidermoid



Phase1 CAGE Peaks

Hg19::chr11:119461966..119461970,+p@chr11:119461966..119461970
+
Hg19::chr11:12211354..12211375,+p@chr11:12211354..12211375
+
Hg19::chr11:12211377..12211384,+p@chr11:12211377..12211384
+
Hg19::chr11:12211454..12211464,+p@chr11:12211454..12211464
+
Hg19::chr11:12211480..12211490,+p@chr11:12211480..12211490
+
Hg19::chr11:393795..393799,-p@chr11:393795..393799
-
Hg19::chr11:64774309..64774333,-p@chr11:64774309..64774333
-
Hg19::chr11:64774372..64774383,-p@chr11:64774372..64774383
-
Hg19::chr11:64774464..64774480,-p@chr11:64774464..64774480
-
Hg19::chr11:65683410..65683420,+p@chr11:65683410..65683420
+
Hg19::chr11:65683428..65683475,+p@chr11:65683428..65683475
+
Hg19::chr11:90222429..90222464,+p@chr11:90222429..90222464
+
Hg19::chr12:65362955..65362961,-p@chr12:65362955..65362961
-
Hg19::chr12:66049021..66049034,-p@chr12:66049021..66049034
-
Hg19::chr12:72104152..72104171,-p1@ENST00000549710
Hg19::chr12:76228513..76228524,-p@chr12:76228513..76228524
-
Hg19::chr12:76228543..76228556,-p@chr12:76228543..76228556
-
Hg19::chr13:74071833..74071844,+p@chr13:74071833..74071844
+
Hg19::chr13:74071854..74071871,+p@chr13:74071854..74071871
+
Hg19::chr13:74071880..74071894,+p@chr13:74071880..74071894
+
Hg19::chr14:29593762..29593772,-p@chr14:29593762..29593772
-
Hg19::chr14:47683291..47683294,-p@chr14:47683291..47683294
-
Hg19::chr14:70466297..70466304,+p@chr14:70466297..70466304
+
Hg19::chr14:71275492..71275543,+p@chr14:71275492..71275543
+
Hg19::chr14:71276610..71276625,+p2@ENST00000554032
Hg19::chr14:71276645..71276721,+p1@ENST00000554032
Hg19::chr15:101417937..101417955,+p8@ALDH1A3
Hg19::chr15:101417973..101417981,+p10@ALDH1A3
Hg19::chr15:101418003..101418019,+p5@ALDH1A3
Hg19::chr15:71389281..71389306,+p4@THSD4
Hg19::chr16:70838983..70838988,-p@chr16:70838983..70838988
-
Hg19::chr16:82671393..82671425,+p@chr16:82671393..82671425
+
Hg19::chr16:82671490..82671521,+p@chr16:82671490..82671521
+
Hg19::chr17:30487950..30487952,-p@chr17:30487950..30487952
-
Hg19::chr17:76506753..76506758,-p11@DNAH17
Hg19::chr19:3656823..3656835,-p@chr19:3656823..3656835
-
Hg19::chr19:39574692..39574701,-p@chr19:39574692..39574701
-
Hg19::chr1:158116675..158116685,-p@chr1:158116675..158116685
-
Hg19::chr1:247692872..247692880,+p@chr1:247692872..247692880
+
Hg19::chr1:55436540..55436544,-p@chr1:55436540..55436544
-
Hg19::chr1:58310606..58310611,-p@chr1:58310606..58310611
-
Hg19::chr20:1459305..1459323,-p@chr20:1459305..1459323
-
Hg19::chr20:49948180..49948199,-p@chr20:49948180..49948199
-
Hg19::chr20:50253078..50253081,+p@chr20:50253078..50253081
+
Hg19::chr3:133199287..133199293,-p@chr3:133199287..133199293
-
Hg19::chr3:162157693..162157708,-p@chr3:162157693..162157708
-
Hg19::chr3:184050382..184050388,+p@chr3:184050382..184050388
+
Hg19::chr3:83227676..83227682,-p@chr3:83227676..83227682
-
Hg19::chr3:8721551..8721586,-p@chr3:8721551..8721586
-
Hg19::chr4:137842587..137842589,-p1@ENST00000512039
Hg19::chr4:149677484..149677487,-p@chr4:149677484..149677487
-
Hg19::chr4:165056668..165056683,-p15@MARCH1
Hg19::chr4:22999152..22999159,+p1@ENST00000511453
p1@uc003gqr.1
Hg19::chr4:75410084..75410098,+p@chr4:75410084..75410098
+
Hg19::chr5:167182003..167182007,-p@chr5:167182003..167182007
-
Hg19::chr5:72598821..72598846,+p@chr5:72598821..72598846
+
Hg19::chr5:72708695..72708700,+p@chr5:72708695..72708700
+
Hg19::chr5:72708745..72708758,+p@chr5:72708745..72708758
+
Hg19::chr5:86415919..86415926,+p1@ENST00000515750
p1@uc003kit.2
Hg19::chr5:8981522..8981557,+p@chr5:8981522..8981557
+
Hg19::chr5:8984611..8984621,-p@chr5:8984611..8984621
-
Hg19::chr5:95404206..95404210,-p@chr5:95404206..95404210
-
Hg19::chr6:143654483..143654535,+p@chr6:143654483..143654535
+
Hg19::chr6:70320255..70320261,-p@chr6:70320255..70320261
-
Hg19::chr7:48075159..48075177,+p2@C7orf57
Hg19::chr7:55775905..55775916,-p@chr7:55775905..55775916
-
Hg19::chr7:64300314..64300319,-p@chr7:64300314..64300319
-
Hg19::chr7:75715539..75715572,-p@chr7:75715539..75715572
-
Hg19::chr7:98805698..98805708,-p@chr7:98805698..98805708
-
Hg19::chr7:98805731..98805743,-p@chr7:98805731..98805743
-
Hg19::chr7:98870435..98870449,+p6@MYH16
Hg19::chr7:98870454..98870479,+p1@MYH16
Hg19::chr7:98870482..98870519,+p2@MYH16
Hg19::chr7:98870526..98870537,+p5@MYH16
Hg19::chr7:98870790..98870795,+p7@MYH16
Hg19::chr7:98870934..98870947,+p4@MYH16
Hg19::chr7:98870948..98870967,+p3@MYH16
Hg19::chr7:98870980..98870981,+p8@MYH16
Hg19::chr8:117456880..117456884,-p@chr8:117456880..117456884
-
Hg19::chr8:123102017..123102025,-p@chr8:123102017..123102025
-
Hg19::chr8:123139536..123139544,-p1@ENST00000523792
p1@uc003ypj.2
Hg19::chr8:126044339..126044344,-p@chr8:126044339..126044344
-
Hg19::chr8:127596030..127596033,+p@chr8:127596030..127596033
+
Hg19::chr8:76774227..76774234,+p@chr8:76774227..76774234
+
Hg19::chr8:87834707..87834714,+p@chr8:87834707..87834714
+
Hg19::chr8:90624105..90624144,-p@chr8:90624105..90624144
-
Hg19::chr9:124328237..124328240,+p@chr9:124328237..124328240
+
Hg19::chrX:19692351..19692356,-p@chrX:19692351..19692356
-
Hg19::chrX:25540398..25540420,+p@chrX:25540398..25540420
+
Hg19::chrX:25540422..25540429,+p@chrX:25540422..25540429
+
Hg19::chrX:29431271..29431280,+p@chrX:29431271..29431280
+
Hg19::chrX:35470106..35470112,+p@chrX:35470106..35470112
+


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:0060166olfactory pit development0.00603402598852654
GO:0002072optic cup morphogenesis involved in camera-type eye development0.00603402598852654
GO:0021768nucleus accumbens development0.00603402598852654
GO:0043584nose development0.00603402598852654
GO:0021756striatum development0.00603402598852654
GO:0048857neural nucleus development0.00603402598852654
GO:0021544subpallium development0.00775757666933773
GO:0048048embryonic eye morphogenesis0.00904997327703826
GO:0042573retinoic acid metabolic process0.0100549338569124
GO:00040283-chloroallyl aldehyde dehydrogenase activity0.0108586892361296
GO:0021761limbic system development0.0115161135774329
GO:0048562embryonic organ morphogenesis0.0150779615211111
GO:0021537telencephalon development0.0153090288070116
GO:0048593camera-type eye morphogenesis0.0167981898572595
GO:0004030aldehyde dehydrogenase [NAD(P)+] activity0.016883340376704
GO:0006776vitamin A metabolic process0.0169577140091317
GO:0006775fat-soluble vitamin metabolic process0.0191488592113784
GO:0048568embryonic organ development0.0200921158836862
GO:0016331morphogenesis of embryonic epithelium0.0209356343747139
GO:0048592eye morphogenesis0.0234994728631865
GO:0043010camera-type eye development0.0292529612633874
GO:0030286dynein complex0.0339912580765414
GO:0030900forebrain development0.0339912580765414
GO:0001654eye development0.0339912580765414
GO:0044430cytoskeletal part0.0339912580765414
GO:0016620oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor0.0347134486806925
GO:0002009morphogenesis of an epithelium0.0420867596980804
GO:0016903oxidoreductase activity, acting on the aldehyde or oxo group of donors0.0463567570676262



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>

Uber Anatomy
Ontology termp-valuen
mammalian vulva1.78e-291
external female genitalia1.78e-291
uterine epithelium2.37e-152
cervix epithelium2.37e-152
tongue8.17e-113
gustatory system8.17e-113
future tongue8.17e-113
mucosa of oral region1.96e-084
respiratory system mucosa1.96e-084
Disease
Ontology termp-valuen
squamous cell carcinoma9.65e-3314
carcinoma5.56e-07106
cervical cancer6.39e-075


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)
MA0003.14.99104e-09
MA0004.11.18494
MA0006.10.0457519
MA0007.10.0490025
MA0009.10.112474
MA0014.11.8067e-07
MA0017.10.0353272
MA0019.10.192717
MA0024.10.068993
MA0025.11.63168
MA0027.11.47809
MA0028.10.0247631
MA0029.10.263395
MA0030.10.53603
MA0031.10.736736
MA0038.11.43522
MA0040.10.569275
MA0041.10.295713
MA0042.10.825469
MA0043.10.732147
MA0046.10.348554
MA0048.10.00208597
MA0050.10.122838
MA0051.10.0504177
MA0052.10.0799011
MA0055.10.0025854
MA0056.10
MA0057.10.00359348
MA0058.12.12212
MA0059.11.14824
MA0060.10.825403
MA0061.10.748833
MA0063.10
MA0066.11.43766
MA0067.10.304116
MA0068.10.0140086
MA0069.10.105679
MA0070.10.330546
MA0071.10.0368616
MA0072.10.0986844
MA0073.12.93657e-06
MA0074.10.0500929
MA0076.10.00615153
MA0077.10.316229
MA0078.10.481625
MA0081.10.314544
MA0083.11.2248
MA0084.10.448027
MA0087.10.32237
MA0088.10.787964
MA0089.10
MA0090.10.595868
MA0091.10.0612406
MA0092.10.09894
MA0093.12.12441
MA0095.10
MA0098.10
MA0100.10.315613
MA0101.10.100637
MA0103.10.68197
MA0105.10.141072
MA0106.16.29814
MA0107.10.382797
MA0108.20.0493529
MA0109.10
MA0111.10.892901
MA0113.10.4014
MA0114.10.0558823
MA0115.10.251028
MA0116.10.032712
MA0117.10.409173
MA0119.10.587735
MA0122.10.443081
MA0124.10.636439
MA0125.10.51417
MA0130.10
MA0131.10.0282896
MA0132.10
MA0133.10
MA0135.10.127133
MA0136.10.0554464
MA0139.10.0153393
MA0140.10.614017
MA0141.10.000585776
MA0142.10.654658
MA0143.10.660354
MA0144.10.132301
MA0145.10.197284
MA0146.10.00438042
MA0147.10.292742
MA0148.11.33601
MA0149.10.00598841
MA0062.20.00865138
MA0035.20.389976
MA0039.27.04958e-06
MA0138.20.258548
MA0002.20.156629
MA0137.20.330221
MA0104.20.188886
MA0047.21.21119
MA0112.20.0387444
MA0065.20.0136882
MA0150.13.22736
MA0151.10
MA0152.10.407566
MA0153.10.490722
MA0154.10.023977
MA0155.10.0183044
MA0156.10.126828
MA0157.10.322729
MA0158.10
MA0159.10.0698723
MA0160.10.190068
MA0161.10
MA0162.18.89507e-06
MA0163.13.45651e-08
MA0164.10.223694
MA0080.20.0964526
MA0018.20.18974
MA0099.25.18072
MA0079.20
MA0102.20.478533
MA0258.10.112859
MA0259.10.0409197
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
FOS#2353212.05388110311720.001001030004563510.00717546826675419
JUN#3725162.176144207362840.002478526449353040.0139229143633811
STAT3#6774222.515524238449934.02961446076117e-050.000738460966252738



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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