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MCL coexpression mm9:274: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000160!1.89e-48!31;UBERON:0005409!3.67e-41!47;UBERON:0000344!2.54e-27!15;UBERON:0001242!1.91e-23!13;UBERON:0000060!1.91e-23!13;UBERON:0001262!1.91e-23!13;UBERON:0004786!1.91e-23!13;UBERON:0003350!1.22e-15!9;UBERON:0004808!1.22e-15!9;UBERON:0001277!1.22e-15!9;UBERON:0004923!1.43e-15!24;UBERON:0001007!9.13e-15!116;UBERON:0001555!9.13e-15!116;UBERON:0007026!9.13e-15!116;UBERON:0004119!2.32e-14!118;UBERON:0000925!2.32e-14!118;UBERON:0006595!2.32e-14!118;UBERON:0004921!8.32e-13!114;UBERON:0000485!1.84e-12!11;UBERON:0002108!2.13e-09!4;UBERON:0000331!1.46e-07!3;UBERON:0002116!1.46e-07!3;UBERON:0001204!1.46e-07!3;UBERON:0001168!1.46e-07!3
|ontology_enrichment_uberon=UBERON:0000160!1.89e-48!31;UBERON:0005409!3.67e-41!47;UBERON:0000344!2.54e-27!15;UBERON:0001242!1.91e-23!13;UBERON:0000060!1.91e-23!13;UBERON:0001262!1.91e-23!13;UBERON:0004786!1.91e-23!13;UBERON:0003350!1.22e-15!9;UBERON:0004808!1.22e-15!9;UBERON:0001277!1.22e-15!9;UBERON:0004923!1.43e-15!24;UBERON:0001007!9.13e-15!116;UBERON:0001555!9.13e-15!116;UBERON:0007026!9.13e-15!116;UBERON:0004119!2.32e-14!118;UBERON:0000925!2.32e-14!118;UBERON:0006595!2.32e-14!118;UBERON:0004921!8.32e-13!114;UBERON:0000485!1.84e-12!11;UBERON:0002108!2.13e-09!4;UBERON:0000331!1.46e-07!3;UBERON:0002116!1.46e-07!3;UBERON:0001204!1.46e-07!3;UBERON:0001168!1.46e-07!3
|tfbs_overrepresentation_for_novel_motifs=0.23755,0.0263039,0.0566731,0.605195,1.08211,0.3086,0.141047,1.57112,0.424301,0.0293535,0.116463,0.417744,0.223136,0.453459,0.269498,0,0.278333,0.0910852,0.192652,0.217457,0.379987,0.316516,0.147721,0.23832,0.21578,0.164963,0.176746,0.336599,0.137229,0.205118,0.0958789,0.937786,0.0893416,0.435403,0.0265392,0.146711,0.0182783,0.412507,0.175879,0.136039,0.44469,0.0984395,2.46709,0.273021,0.188752,0.0805114,0.22117,0.358188,1.21937,0.140032,0.265451,0.181937,0.188595,0.473629,0.488593,0.152527,0.0376921,0.126922,0.477812,0.151304,0.340494,0.18804,0.463996,0.257242,0.159274,0.782577,0.608645,0.933761,0.336817,0.794446,0.186282,0.923941,0.010253,0.517629,0.0654223,0.859617,0.435115,0.213375,0.327041,0.68941,0.113052,0.291331,1.04732,0.851995,0.419339,9.42369e-06,1.03644,0.755383,0.224557,1.0899,0.671836,0.423481,0.366627,0.471953,0.0643175,0.503507,0.385489,0.368885,0.221346,0.852256,0.662988,0.356153,0.458781,0.265886,0.265114,0.0982201,0.309919,0.108981,0.0466454,0.16918,0.495806,0.460295,0.172898,0.119253,0.678281,0.715266,0.0403473,0.0874099,0.279301,0.393671,0.522338,0.67935,0.166093,0.212759,0.728107,0.329926,0.145825,0.361192,0.607282,0.480235,0.444416,0.0822682,0.580825,0.940463,0.698098,0.00816231,0.529534,0.669918,0.653122,1.45055,1.05907,0.612882,0.516217,0.956294,0.260385,0.32519,0.223324,1.41144,0.250541,0.0228418,0.211386,0.00015102,1.19589,0.0116955,0.938112,0.545909,0.537994,0.121837,1.31001,0.0704805,0.661783,0.418628,0.330273,0.063259,2.0361,0.472114,0.400434,0.415443,0.351528
|tfbs_overrepresentation_for_novel_motifs=0.23755,0.0263039,0.0566731,0.605195,1.08211,0.3086,0.141047,1.57112,0.424301,0.0293535,0.116463,0.417744,0.223136,0.453459,0.269498,0,0.278333,0.0910852,0.192652,0.217457,0.379987,0.316516,0.147721,0.23832,0.21578,0.164963,0.176746,0.336599,0.137229,0.205118,0.0958789,0.937786,0.0893416,0.435403,0.0265392,0.146711,0.0182783,0.412507,0.175879,0.136039,0.44469,0.0984395,2.46709,0.273021,0.188752,0.0805114,0.22117,0.358188,1.21937,0.140032,0.265451,0.181937,0.188595,0.473629,0.488593,0.152527,0.0376921,0.126922,0.477812,0.151304,0.340494,0.18804,0.463996,0.257242,0.159274,0.782577,0.608645,0.933761,0.336817,0.794446,0.186282,0.923941,0.010253,0.517629,0.0654223,0.859617,0.435115,0.213375,0.327041,0.68941,0.113052,0.291331,1.04732,0.851995,0.419339,9.42369e-06,1.03644,0.755383,0.224557,1.0899,0.671836,0.423481,0.366627,0.471953,0.0643175,0.503507,0.385489,0.368885,0.221346,0.852256,0.662988,0.356153,0.458781,0.265886,0.265114,0.0982201,0.309919,0.108981,0.0466454,0.16918,0.495806,0.460295,0.172898,0.119253,0.678281,0.715266,0.0403473,0.0874099,0.279301,0.393671,0.522338,0.67935,0.166093,0.212759,0.728107,0.329926,0.145825,0.361192,0.607282,0.480235,0.444416,0.0822682,0.580825,0.940463,0.698098,0.00816231,0.529534,0.669918,0.653122,1.45055,1.05907,0.612882,0.516217,0.956294,0.260385,0.32519,0.223324,1.41144,0.250541,0.0228418,0.211386,0.00015102,1.19589,0.0116955,0.938112,0.545909,0.537994,0.121837,1.31001,0.0704805,0.661783,0.418628,0.330273,0.063259,2.0361,0.472114,0.400434,0.415443,0.351528
|tfbs_overrepresentation_jaspar=MA0003.1;0.000637416,MA0004.1;0.0858689,MA0006.1;0.489667,MA0007.1;0.271387,MA0009.1;0.98466,MA0014.1;0.000363139,MA0017.1;0.565651,MA0019.1;0.238713,MA0024.1;0.342622,MA0025.1;0.57681,MA0027.1;1.94532,MA0028.1;0.0279413,MA0029.1;0.325591,MA0030.1;0.330711,MA0031.1;0.819094,MA0038.1;1.52625,MA0040.1;0.387805,MA0041.1;0.0540602,MA0042.1;0.184959,MA0043.1;0.457929,MA0046.1;0.407017,MA0048.1;0.432462,MA0050.1;1.15074,MA0051.1;0.170484,MA0052.1;0.394392,MA0055.1;2.3003,MA0056.1;0,MA0057.1;0.133583,MA0058.1;0.0469235,MA0059.1;0.190935,MA0060.1;0.010101,MA0061.1;0.0691531,MA0063.1;0,MA0066.1;2.13057,MA0067.1;0.677115,MA0068.1;0.0690941,MA0069.1;0.39467,MA0070.1;0.386747,MA0071.1;0.104441,MA0072.1;0.379853,MA0073.1;0.00623528,MA0074.1;1.35784,MA0076.1;0.149319,MA0077.1;0.36238,MA0078.1;0.191654,MA0081.1;1.2432,MA0083.1;1.15781,MA0084.1;0.985399,MA0087.1;0.421024,MA0088.1;0.123781,MA0089.1;0,MA0090.1;0.070593,MA0091.1;2.15074,MA0092.1;0.530193,MA0093.1;0.123866,MA0095.1;0,MA0098.1;0,MA0100.1;0.408164,MA0101.1;0.0545406,MA0103.1;1.34399,MA0105.1;0.0180499,MA0106.1;0.196768,MA0107.1;0.135394,MA0108.2;0.255046,MA0109.1;0,MA0111.1;0.265025,MA0113.1;3.0387,MA0114.1;0.349749,MA0115.1;0.460306,MA0116.1;0.0252794,MA0117.1;0.433078,MA0119.1;0.201463,MA0122.1;0.449781,MA0124.1;0.628716,MA0125.1;0.562419,MA0130.1;0,MA0131.1;0.235509,MA0132.1;0,MA0133.1;0,MA0135.1;0.489063,MA0136.1;0.889206,MA0139.1;0.100346,MA0140.1;1.31637,MA0141.1;0.160688,MA0142.1;0.292245,MA0143.1;0.188991,MA0144.1;0.595811,MA0145.1;0.144964,MA0146.1;0.0027874,MA0147.1;0.200453,MA0148.1;1.58531,MA0149.1;0.0566148,MA0062.2;0.0627172,MA0035.2;1.92936,MA0039.2;0.0011259,MA0138.2;0.229939,MA0002.2;1.2015,MA0137.2;0.157757,MA0104.2;0.251331,MA0047.2;1.52347,MA0112.2;0.011779,MA0065.2;0.145939,MA0150.1;0.0789524,MA0151.1;0,MA0152.1;0.164506,MA0153.1;0.503426,MA0154.1;0.0756214,MA0155.1;0.0462202,MA0156.1;0.969141,MA0157.1;0.26838,MA0158.1;0,MA0159.1;0.0857096,MA0160.1;0.315504,MA0161.1;0,MA0162.1;0.00036638,MA0163.1;0.00358873,MA0164.1;0.454747,MA0080.2;0.581847,MA0018.2;0.154575,MA0099.2;0.22555,MA0079.2;4.11922e-11,MA0102.2;1.03585,MA0258.1;0.535442,MA0259.1;0.0707314,MA0442.1;0
}}
}}

Revision as of 11:28, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:101953059..101953074,-p1@Nts
Mm9::chr11:75381481..75381495,+p@chr11:75381481..75381495
+
Mm9::chr15:58341592..58341608,+p1@Fer1l6
Mm9::chr15:75759076..75759118,-p@chr15:75759076..75759118
-
Mm9::chr15:99058963..99058972,+p@chr15:99058963..99058972
+
Mm9::chr16:33518275..33518293,+p1@Slc12a8
Mm9::chr16:33518389..33518426,+p2@Slc12a8
Mm9::chr17:25507495..25507511,+p5@Tpsg1
Mm9::chr17:25507520..25507544,+p2@Tpsg1
Mm9::chr17:29430984..29431005,+p@chr17:29430984..29431005
+
Mm9::chr3:144672785..144672802,-p@chr3:144672785..144672802
-
Mm9::chr3:144672850..144672861,-p@chr3:144672850..144672861
-
Mm9::chr3:144681646..144681660,-p@chr3:144681646..144681660
-
Mm9::chr3:144687544..144687560,-p@chr3:144687544..144687560
-
Mm9::chr3:144690317..144690343,+p@chr3:144690317..144690343
+
Mm9::chr3:144695729..144695745,-p1@Clca3
Mm9::chr3:144695833..144695862,-p3@Clca3
Mm9::chr3:144695921..144695933,-p2@Clca3
Mm9::chr4:40867080..40867096,+p1@Spink4
Mm9::chr4:40878323..40878351,-p@chr4:40878323..40878351
-
Mm9::chr6:3444486..3444526,-p1@Hepacam2
Mm9::chr6:3444527..3444542,-p2@Hepacam2
Mm9::chr6:3444549..3444563,-p4@Hepacam2
Mm9::chr6:3444587..3444598,-p3@Hepacam2
Mm9::chr6:64679112..64679126,+p1@Atoh1
Mm9::chr7:148876232..148876247,+p1@Muc2
Mm9::chr7:148878517..148878527,+p@chr7:148878517..148878527
+
Mm9::chr7:148880479..148880493,+p@chr7:148880479..148880493
+
Mm9::chr7:28886314..28886326,+p4@Fcgbp
Mm9::chr8:12931718..12931750,+p@chr8:12931718..12931750
+


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:0042667auditory receptor cell fate specification0.0237659562811593
GO:0045633positive regulation of mechanoreceptor differentiation0.0237659562811593
GO:0045606positive regulation of epidermal cell differentiation0.0237659562811593
GO:0045609positive regulation of auditory receptor cell differentiation0.0237659562811593
GO:0045684positive regulation of epidermis development0.0237659562811593
GO:0042668auditory receptor cell fate determination0.0445416390019618
GO:0045607regulation of auditory receptor cell differentiation0.0445416390019618
GO:0045631regulation of mechanoreceptor differentiation0.0445416390019618



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>cell_data<br>uberon_data<br><br>


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)
MA0003.10.000637416
MA0004.10.0858689
MA0006.10.489667
MA0007.10.271387
MA0009.10.98466
MA0014.10.000363139
MA0017.10.565651
MA0019.10.238713
MA0024.10.342622
MA0025.10.57681
MA0027.11.94532
MA0028.10.0279413
MA0029.10.325591
MA0030.10.330711
MA0031.10.819094
MA0038.11.52625
MA0040.10.387805
MA0041.10.0540602
MA0042.10.184959
MA0043.10.457929
MA0046.10.407017
MA0048.10.432462
MA0050.11.15074
MA0051.10.170484
MA0052.10.394392
MA0055.12.3003
MA0056.10
MA0057.10.133583
MA0058.10.0469235
MA0059.10.190935
MA0060.10.010101
MA0061.10.0691531
MA0063.10
MA0066.12.13057
MA0067.10.677115
MA0068.10.0690941
MA0069.10.39467
MA0070.10.386747
MA0071.10.104441
MA0072.10.379853
MA0073.10.00623528
MA0074.11.35784
MA0076.10.149319
MA0077.10.36238
MA0078.10.191654
MA0081.11.2432
MA0083.11.15781
MA0084.10.985399
MA0087.10.421024
MA0088.10.123781
MA0089.10
MA0090.10.070593
MA0091.12.15074
MA0092.10.530193
MA0093.10.123866
MA0095.10
MA0098.10
MA0100.10.408164
MA0101.10.0545406
MA0103.11.34399
MA0105.10.0180499
MA0106.10.196768
MA0107.10.135394
MA0108.20.255046
MA0109.10
MA0111.10.265025
MA0113.13.0387
MA0114.10.349749
MA0115.10.460306
MA0116.10.0252794
MA0117.10.433078
MA0119.10.201463
MA0122.10.449781
MA0124.10.628716
MA0125.10.562419
MA0130.10
MA0131.10.235509
MA0132.10
MA0133.10
MA0135.10.489063
MA0136.10.889206
MA0139.10.100346
MA0140.11.31637
MA0141.10.160688
MA0142.10.292245
MA0143.10.188991
MA0144.10.595811
MA0145.10.144964
MA0146.10.0027874
MA0147.10.200453
MA0148.11.58531
MA0149.10.0566148
MA0062.20.0627172
MA0035.21.92936
MA0039.20.0011259
MA0138.20.229939
MA0002.21.2015
MA0137.20.157757
MA0104.20.251331
MA0047.21.52347
MA0112.20.011779
MA0065.20.145939
MA0150.10.0789524
MA0151.10
MA0152.10.164506
MA0153.10.503426
MA0154.10.0756214
MA0155.10.0462202
MA0156.10.969141
MA0157.10.26838
MA0158.10
MA0159.10.0857096
MA0160.10.315504
MA0161.10
MA0162.10.00036638
MA0163.10.00358873
MA0164.10.454747
MA0080.20.581847
MA0018.20.154575
MA0099.20.22555
MA0079.24.11922e-11
MA0102.21.03585
MA0258.10.535442
MA0259.10.0707314
MA0442.10
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