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MCL coexpression mm9:174: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!4.76e-08!73;UBERON:0001016!2.77e-07!75
|tfbs_overrepresentation_for_novel_motifs=0.253866,0.0118384,0.209165,0.561854,0.00711284,0.906355,0.134211,0.630422,0.0833305,0.015386,0.248832,0.296559,0.0341804,0.95133,0.288969,0,0.347413,1.58468,0.0251736,0.0831246,0.153587,0.244396,0.143541,1.64528,1.567,0.381817,0.0464871,1.80031,0.048247,0.117658,0.378945,1.4945,0.124167,0.0307183,0.0335546,1.6157e-06,0.0049929,0.290961,0.0832206,0.0537501,0.555846,0.201191,0.706677,0.903252,0.0133567,0.528808,0.254098,0.445193,0.160718,0.377496,0.669018,0.752602,0.0309672,0.692511,0.259778,0.977121,2.6527,2.09755,0.59236,0.96974,0.453716,1.66618,0.050028,0.645208,0.0412534,0.112603,0.359348,0.65247,0.145808,0.523767,0.00474628,0.0380694,0.000101673,0.283239,0.00515595,0.00372651,0.6867,0.241795,0.43036,0.159517,1.37174,1.22023,0.201227,0.0637118,0.20577,1.63916e-06,0.0127266,0.0172882,1.40129,0.800315,0.414101,0.208915,0.499559,0.149032,0.980833,0.025894,1.83563,0.503548,0.541682,3.61975e-05,0.201754,0.159361,0.23617,1.11223,1.10894,0.200619,0.127528,0.091635,0.305256,0.00377432,0.115101,0.668082,0.00397509,0.256313,0.41976,1.00882,3.69415e-07,2.51343,0.107616,0.0493429,0.287084,0.287827,0.0444158,0.517087,0.463931,0.141059,0.32868,0.162947,2.53434,0.845272,0.639118,0.540144,0.335709,0.661279,0.437241,6.23987e-05,0.0470311,0.39316,0.397743,1.15036,0.770879,1.69673,2.07025,0.49625,0.0958394,0.0173511,0.54736,1.11202,0.133128,0.00733256,0.00742599,3.44657e-05,0.248928,0.339845,0.041699,0.826428,1.62507,0.0956645,0.673517,0.0469068,0.4053,2.47974,0.141297,0.112917,0.0943743,0.0396464,0.109408,0.0300011,0.0132865
|tfbs_overrepresentation_jaspar=MA0003.1;0.0287981,MA0004.1;0.0637743,MA0006.1;0.0790063,MA0007.1;0.011467,MA0009.1;0.519036,MA0014.1;0.00381863,MA0017.1;0.349752,MA0019.1;0.99639,MA0024.1;0.457425,MA0025.1;0.884344,MA0027.1;1.63967,MA0028.1;0.036159,MA0029.1;0.427852,MA0030.1;0.141597,MA0031.1;0.77915,MA0038.1;0.168207,MA0040.1;0.182227,MA0041.1;0.197994,MA0042.1;0.177712,MA0043.1;0.663757,MA0046.1;0.196485,MA0048.1;0.0095511,MA0050.1;0.21804,MA0051.1;0.397275,MA0052.1;0.187085,MA0055.1;0.00264065,MA0056.1;0,MA0057.1;0.00641833,MA0058.1;0.307133,MA0059.1;0.784311,MA0060.1;0.0235683,MA0061.1;0.162887,MA0063.1;0,MA0066.1;0.158428,MA0067.1;0.418736,MA0068.1;0.00269202,MA0069.1;0.549379,MA0070.1;0.18145,MA0071.1;0.216913,MA0072.1;0.176408,MA0073.1;7.51837e-05,MA0074.1;0.557689,MA0076.1;0.12985,MA0077.1;0.492069,MA0078.1;0.794498,MA0081.1;0.890874,MA0083.1;0.234977,MA0084.1;0.70101,MA0087.1;0.59672,MA0088.1;0.00111008,MA0089.1;0,MA0090.1;2.19351,MA0091.1;0.362524,MA0092.1;0.465225,MA0093.1;0.011735,MA0095.1;0,MA0098.1;0,MA0100.1;0.0288553,MA0101.1;0.00566999,MA0103.1;0.381239,MA0105.1;0.251305,MA0106.1;0.215981,MA0107.1;0.0140932,MA0108.2;0.0925928,MA0109.1;0,MA0111.1;0.145795,MA0113.1;0.188199,MA0114.1;0.037977,MA0115.1;0.237365,MA0116.1;0.00871944,MA0117.1;0.216245,MA0119.1;1.13194,MA0122.1;0.229146,MA0124.1;0.376587,MA0125.1;0.320242,MA0130.1;0,MA0131.1;0.0810237,MA0132.1;0,MA0133.1;0,MA0135.1;0.720903,MA0136.1;0.036462,MA0139.1;0.00373761,MA0140.1;0.841906,MA0141.1;0.658771,MA0142.1;3.86671,MA0143.1;1.19419,MA0144.1;0.087955,MA0145.1;0.675916,MA0146.1;0.00568788,MA0147.1;0.0480289,MA0148.1;0.188634,MA0149.1;0.00609102,MA0062.2;0.000229611,MA0035.2;0.123099,MA0039.2;1.58775e-08,MA0138.2;0.0778187,MA0002.2;1.03897,MA0137.2;0.00319383,MA0104.2;0.00568325,MA0047.2;0.0436413,MA0112.2;0.831033,MA0065.2;0.0685068,MA0150.1;0.305334,MA0151.1;0,MA0152.1;0.380541,MA0153.1;2.10674,MA0154.1;0.495717,MA0155.1;0.0178721,MA0156.1;0.00276165,MA0157.1;0.330817,MA0158.1;0,MA0159.1;0.211707,MA0160.1;0.0745345,MA0161.1;0,MA0162.1;5.07525e-07,MA0163.1;0.156187,MA0164.1;0.0365559,MA0080.2;0.0142719,MA0018.2;0.0391256,MA0099.2;0.553751,MA0079.2;2.46675e-11,MA0102.2;0.74879,MA0258.1;2.08808,MA0259.1;0.167485,MA0442.1;0
}}

Latest revision as of 14:49, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:104675544..104675572,+p@chr10:104675544..104675572
+
Mm9::chr10:26327900..26327901,+p@chr10:26327900..26327901
+
Mm9::chr11:108873019..108873046,-p@chr11:108873019..108873046
-
Mm9::chr11:108873085..108873096,-p@chr11:108873085..108873096
-
Mm9::chr11:108873174..108873185,-p@chr11:108873174..108873185
-
Mm9::chr11:108873217..108873254,-p@chr11:108873217..108873254
-
Mm9::chr11:108873302..108873314,-p@chr11:108873302..108873314
-
Mm9::chr11:17121426..17121456,+p@chr11:17121426..17121456
+
Mm9::chr11:95942492..95942530,+p@chr11:95942492..95942530
+
Mm9::chr12:100883434..100883465,+p@chr12:100883434..100883465
+
Mm9::chr12:100883758..100883774,+p@chr12:100883758..100883774
+
Mm9::chr12:55236145..55236157,+p@chr12:55236145..55236157
+
Mm9::chr12:81542532..81542533,-p@chr12:81542532..81542533
-
Mm9::chr13:44964977..44964992,-p@chr13:44964977..44964992
-
Mm9::chr13:44965056..44965083,-p@chr13:44965056..44965083
-
Mm9::chr13:44965087..44965098,-p@chr13:44965087..44965098
-
Mm9::chr13:54285345..54285377,-p@chr13:54285345..54285377
-
Mm9::chr13:54285541..54285556,-p@chr13:54285541..54285556
-
Mm9::chr13:97960521..97960565,-p@chr13:97960521..97960565
-
Mm9::chr14:20110662..20110693,+p@chr14:20110662..20110693
+
Mm9::chr14:57312922..57312954,-p@chr14:57312922..57312954
-
Mm9::chr15:78668246..78668247,-p@chr15:78668246..78668247
-
Mm9::chr16:35981679..35981717,+p@chr16:35981679..35981717
+
Mm9::chr16:35981824..35981855,-p@chr16:35981824..35981855
-
Mm9::chr16:57391566..57391605,-p@chr16:57391566..57391605
-
Mm9::chr17:14649861..14649863,+p@chr17:14649861..14649863
+
Mm9::chr17:23013421..23013445,+p@chr17:23013421..23013445
+
Mm9::chr17:71312999..71313007,+p@chr17:71312999..71313007
+
Mm9::chr18:54858791..54858830,-p@chr18:54858791..54858830
-
Mm9::chr18:68851751..68851784,+p@chr18:68851751..68851784
+
Mm9::chr18:85867345..85867368,-p@chr18:85867345..85867368
-
Mm9::chr18:85867422..85867454,-p@chr18:85867422..85867454
-
Mm9::chr18:85867499..85867530,-p@chr18:85867499..85867530
-
Mm9::chr19:22926471..22926512,+p@chr19:22926471..22926512
+
Mm9::chr19:40194237..40194255,+p@chr19:40194237..40194255
+
Mm9::chr19:40194276..40194311,+p@chr19:40194276..40194311
+
Mm9::chr19:51217168..51217185,-p@chr19:51217168..51217185
-
Mm9::chr19:8326763..8326780,-p@chr19:8326763..8326780
-
Mm9::chr1:102076839..102076885,-p@chr1:102076839..102076885
-
Mm9::chr1:124253801..124253823,-p@chr1:124253801..124253823
-
Mm9::chr1:192944928..192944957,+p@chr1:192944928..192944957
+
Mm9::chr1:46132866..46132898,-p@chr1:46132866..46132898
-
Mm9::chr2:102669618..102669628,-p@chr2:102669618..102669628
-
Mm9::chr2:124315917..124315919,-p@chr2:124315917..124315919
-
Mm9::chr2:148325722..148325726,+p@chr2:148325722..148325726
+
Mm9::chr2:5300382..5300406,-p@chr2:5300382..5300406
-
Mm9::chr2:72850967..72850983,-p1@ENSMUST00000175243
Mm9::chr3:37380275..37380294,+p2@ENSMUST00000121415
Mm9::chr3:37380392..37380415,+p1@ENSMUST00000121415
Mm9::chr3:37380481..37380492,+p5@ENSMUST00000121415
Mm9::chr3:5860668..5860718,+p@chr3:5860668..5860718
+
Mm9::chr4:128485623..128485630,+p@chr4:128485623..128485630
+
Mm9::chr5:143916374..143916383,-p@chr5:143916374..143916383
-
Mm9::chr6:109455149..109455185,-p@chr6:109455149..109455185
-
Mm9::chr7:140501436..140501438,+p@chr7:140501436..140501438
+
Mm9::chr9:123371193..123371208,+p@chr9:123371193..123371208
+
Mm9::chr9:3258604..3258629,-p@chr9:3258604..3258629
-
Mm9::chr9:3260872..3260875,-p@chr9:3260872..3260875
-
Mm9::chr9:41742134..41742136,-p@chr9:41742134..41742136
-
Mm9::chrX:3846730..3846751,+p@chrX:3846730..3846751
+
Mm9::chrX:4545392..4545412,+p@chrX:4545392..4545412
+


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

GO IDGO nameFDR corrected p-value
GO:0006429leucyl-tRNA aminoacylation0.0118333470026975
GO:0004823leucine-tRNA ligase activity0.0118333470026975
GO:0004727prenylated protein tyrosine phosphatase activity0.0315504052129011
GO:0004089carbonate dehydratase activity0.0473100474364755
GO:0007185transmembrane receptor protein tyrosine phosphatase signaling pathway0.0473100474364755
GO:0043038amino acid activation0.0482572857440634
GO:0043039tRNA aminoacylation0.0482572857440634
GO:0006418tRNA aminoacylation for protein translation0.0482572857440634
GO:0016875ligase activity, forming carbon-oxygen bonds0.0482572857440634
GO:0016876ligase activity, forming aminoacyl-tRNA and related compounds0.0482572857440634
GO:0016836hydro-lyase activity0.0482572857440634
GO:0004812aminoacyl-tRNA ligase activity0.0482572857440634



Relative expression of the co-expression cluster over median <br>Analyst:




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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
central nervous system4.76e-0873
nervous system2.77e-0775


TFBS overrepresentation<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)
MA0003.10.0287981
MA0004.10.0637743
MA0006.10.0790063
MA0007.10.011467
MA0009.10.519036
MA0014.10.00381863
MA0017.10.349752
MA0019.10.99639
MA0024.10.457425
MA0025.10.884344
MA0027.11.63967
MA0028.10.036159
MA0029.10.427852
MA0030.10.141597
MA0031.10.77915
MA0038.10.168207
MA0040.10.182227
MA0041.10.197994
MA0042.10.177712
MA0043.10.663757
MA0046.10.196485
MA0048.10.0095511
MA0050.10.21804
MA0051.10.397275
MA0052.10.187085
MA0055.10.00264065
MA0056.10
MA0057.10.00641833
MA0058.10.307133
MA0059.10.784311
MA0060.10.0235683
MA0061.10.162887
MA0063.10
MA0066.10.158428
MA0067.10.418736
MA0068.10.00269202
MA0069.10.549379
MA0070.10.18145
MA0071.10.216913
MA0072.10.176408
MA0073.17.51837e-05
MA0074.10.557689
MA0076.10.12985
MA0077.10.492069
MA0078.10.794498
MA0081.10.890874
MA0083.10.234977
MA0084.10.70101
MA0087.10.59672
MA0088.10.00111008
MA0089.10
MA0090.12.19351
MA0091.10.362524
MA0092.10.465225
MA0093.10.011735
MA0095.10
MA0098.10
MA0100.10.0288553
MA0101.10.00566999
MA0103.10.381239
MA0105.10.251305
MA0106.10.215981
MA0107.10.0140932
MA0108.20.0925928
MA0109.10
MA0111.10.145795
MA0113.10.188199
MA0114.10.037977
MA0115.10.237365
MA0116.10.00871944
MA0117.10.216245
MA0119.11.13194
MA0122.10.229146
MA0124.10.376587
MA0125.10.320242
MA0130.10
MA0131.10.0810237
MA0132.10
MA0133.10
MA0135.10.720903
MA0136.10.036462
MA0139.10.00373761
MA0140.10.841906
MA0141.10.658771
MA0142.13.86671
MA0143.11.19419
MA0144.10.087955
MA0145.10.675916
MA0146.10.00568788
MA0147.10.0480289
MA0148.10.188634
MA0149.10.00609102
MA0062.20.000229611
MA0035.20.123099
MA0039.21.58775e-08
MA0138.20.0778187
MA0002.21.03897
MA0137.20.00319383
MA0104.20.00568325
MA0047.20.0436413
MA0112.20.831033
MA0065.20.0685068
MA0150.10.305334
MA0151.10
MA0152.10.380541
MA0153.12.10674
MA0154.10.495717
MA0155.10.0178721
MA0156.10.00276165
MA0157.10.330817
MA0158.10
MA0159.10.211707
MA0160.10.0745345
MA0161.10
MA0162.15.07525e-07
MA0163.10.156187
MA0164.10.0365559
MA0080.20.0142719
MA0018.20.0391256
MA0099.20.553751
MA0079.22.46675e-11
MA0102.20.74879
MA0258.12.08808
MA0259.10.167485
MA0442.10
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