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MCL coexpression mm9:1043: Difference between revisions

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|ontology_enrichment_uberon=
|ontology_enrichment_uberon=
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.369498,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.215218,0.478312,0.542749,0.575086,0.206435,0.599731,0.315771,0,1.86712,0.291368,0.561256,0.731589,0.374752,0.27937,0.598814,0.80655,1.07577,0.62766,0.184473,0.516511,0.344372,0.876948,0.50223,0.897561,0.78719,0.498917,0.316253,0.248902,0.766323,0.57142,0.258564,0.230656,0.800988,0.507468,0.0742755,0.317766,0.515031,0.469348,0.714592,0.532496,0.0609361,0.347313,0.777641,1.57618,0.431711,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,1.47148,0.877332,0.664501,0.226529,0.766235,1.49952,0.807219,1.19497,1.54543,0.872612,1.39786,1.01778,0.21183,0.611537,1.09164,0.507615,0.482617,0.166511,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,0.200155,0.975495,1.84334,0.374181,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.708155,0.237542,0.203879,0.913319,0.71485,0.399703,0.7665,0.897279,2.33242,0.778243,0.777175,1.26443,0.837607,0.528416,0.383871,0.982279,1.10097,1.02459,0.380122,1.35148,1.27206,0.293461,0.735764,0.484437,1.86983,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,2.08944,2.67845,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,1.13474,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.886471,0.927167,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,1.09603,0.767269,0.612377,0.278874,0.573477,0.0907999
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.369498,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.215218,0.478312,0.542749,0.575086,0.206435,0.599731,0.315771,0,1.86712,0.291368,0.561256,0.731589,0.374752,0.27937,0.598814,0.80655,1.07577,0.62766,0.184473,0.516511,0.344372,0.876948,0.50223,0.897561,0.78719,0.498917,0.316253,0.248902,0.766323,0.57142,0.258564,0.230656,0.800988,0.507468,0.0742755,0.317766,0.515031,0.469348,0.714592,0.532496,0.0609361,0.347313,0.777641,1.57618,0.431711,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,1.47148,0.877332,0.664501,0.226529,0.766235,1.49952,0.807219,1.19497,1.54543,0.872612,1.39786,1.01778,0.21183,0.611537,1.09164,0.507615,0.482617,0.166511,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,0.200155,0.975495,1.84334,0.374181,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.708155,0.237542,0.203879,0.913319,0.71485,0.399703,0.7665,0.897279,2.33242,0.778243,0.777175,1.26443,0.837607,0.528416,0.383871,0.982279,1.10097,1.02459,0.380122,1.35148,1.27206,0.293461,0.735764,0.484437,1.86983,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,2.08944,2.67845,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,1.13474,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.886471,0.927167,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,1.09603,0.767269,0.612377,0.278874,0.573477,0.0907999
|tfbs_overrepresentation_jaspar=MA0003.1;0.188259,MA0004.1;0.481116,MA0006.1;1.51462,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;0.222567,MA0017.1;0.337808,MA0019.1;0.740036,MA0024.1;2.04116,MA0025.1;1.15921,MA0027.1;2.57545,MA0028.1;2.35736,MA0029.1;0.858105,MA0030.1;0.864739,MA0031.1;0.828781,MA0038.1;0.62758,MA0040.1;0.936879,MA0041.1;0.404721,MA0042.1;0.391504,MA0043.1;1.02178,MA0046.1;0.960497,MA0048.1;0.801219,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;0.362005,MA0056.1;0,MA0057.1;0.376102,MA0058.1;1.00014,MA0059.1;0.397033,MA0060.1;1.90283,MA0061.1;0.261749,MA0063.1;0,MA0066.1;0.616444,MA0067.1;1.27078,MA0068.1;0.121435,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;0.519509,MA0072.1;0.927016,MA0073.1;0.0210304,MA0074.1;0.580087,MA0076.1;0.938908,MA0077.1;0.905143,MA0078.1;0.670113,MA0081.1;1.07783,MA0083.1;1.02098,MA0084.1;1.59945,MA0087.1;0.977537,MA0088.1;0.598004,MA0089.1;0,MA0090.1;0.446539,MA0091.1;0.494398,MA0092.1;0.446857,MA0093.1;0.879104,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;0.406019,MA0103.1;0.348572,MA0105.1;0.162418,MA0106.1;0.677988,MA0107.1;0.342432,MA0108.2;0.763162,MA0109.1;0,MA0111.1;0.460823,MA0113.1;0.649407,MA0114.1;0.259463,MA0115.1;1.0246,MA0116.1;0.311187,MA0117.1;0.992087,MA0119.1;0.40661,MA0122.1;1.01209,MA0124.1;1.21735,MA0125.1;1.14291,MA0130.1;0,MA0131.1;1.74348,MA0132.1;0,MA0133.1;0,MA0135.1;1.05845,MA0136.1;0.600242,MA0139.1;0.585936,MA0140.1;0.568252,MA0141.1;0.368264,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.262477,MA0145.1;0.631666,MA0146.1;0.493711,MA0147.1;0.753844,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;2.93496,MA0035.2;0.573016,MA0039.2;1.72008,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;0.365364,MA0104.2;1.17226,MA0047.2;0.626803,MA0112.2;0.0910939,MA0065.2;0.0914071,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.126143,MA0155.1;0.102995,MA0156.1;0.936991,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.776527,MA0160.1;0.50056,MA0161.1;0,MA0162.1;1.26636,MA0163.1;0.116706,MA0164.1;0.600609,MA0080.2;0.908823,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;0.323753,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;0.729797,MA0442.1;0
}}
}}

Revision as of 12:43, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:80261375..80261387,+p2@Sf3a2
Mm9::chr13:74075209..74075235,-p3@Trip13
Mm9::chr17:25864309..25864371,-p1@Chtf18
Mm9::chr17:35118843..35118885,+p2@Lsm2
Mm9::chr17:56179847..56179868,+p2@Chaf1a
Mm9::chr19:6085039..6085051,+p2@Cdca5
Mm9::chr4:124614077..124614088,-p2@Cdca8


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:0000375RNA splicing, via transesterification reactions0.00366088563816577
GO:0000398nuclear mRNA splicing, via spliceosome0.00366088563816577
GO:0000377RNA splicing, via transesterification reactions with bulged adenosine as nucleophile0.00366088563816577
GO:0000351assembly of spliceosomal tri-snRNP U4/U6.U50.0157720689898799
GO:0006374nuclear mRNA splicing via U2-type spliceosome0.0157720689898799
GO:0000387spliceosomal snRNP biogenesis0.0157720689898799
GO:0000244assembly of spliceosomal tri-snRNP0.0157720689898799
GO:0005681spliceosome0.0157720689898799
GO:0007067mitosis0.0157720689898799
GO:0007049cell cycle0.0157720689898799
GO:0000087M phase of mitotic cell cycle0.0157720689898799
GO:0008380RNA splicing0.0157720689898799
GO:0046540U4/U6 x U5 tri-snRNP complex0.0157720689898799
GO:0000278mitotic cell cycle0.0207318967750936
GO:0006397mRNA processing0.0207318967750936
GO:0000279M phase0.0207318967750936
GO:0051301cell division0.0207318967750936
GO:0016071mRNA metabolic process0.0229934679448512
GO:0030532small nuclear ribonucleoprotein complex0.023320273436187
GO:0022403cell cycle phase0.023320273436187
GO:0031202RNA splicing factor activity, transesterification mechanism0.023405844151925
GO:0005634nucleus0.0319252401371916
GO:0006396RNA processing0.0330509239918394
GO:0006402mRNA catabolic process0.0476614567240531
GO:0030529ribonucleoprotein complex0.0487217682126219



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><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)
MA0003.10.188259
MA0004.10.481116
MA0006.11.51462
MA0007.10.465969
MA0009.10.92425
MA0014.10.222567
MA0017.10.337808
MA0019.10.740036
MA0024.12.04116
MA0025.11.15921
MA0027.12.57545
MA0028.12.35736
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.10.801219
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.362005
MA0056.10
MA0057.10.376102
MA0058.11.00014
MA0059.10.397033
MA0060.11.90283
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.121435
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.0210304
MA0074.10.580087
MA0076.10.938908
MA0077.10.905143
MA0078.10.670113
MA0081.11.07783
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.598004
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.10.879104
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.162418
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.259463
MA0115.11.0246
MA0116.10.311187
MA0117.10.992087
MA0119.10.40661
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.11.74348
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.10.585936
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.631666
MA0146.10.493711
MA0147.10.753844
MA0148.10.49752
MA0149.10.411562
MA0062.22.93496
MA0035.20.573016
MA0039.21.72008
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.21.17226
MA0047.20.626803
MA0112.20.0910939
MA0065.20.0914071
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.126143
MA0155.10.102995
MA0156.10.936991
MA0157.10.781683
MA0158.10
MA0159.10.776527
MA0160.10.50056
MA0161.10
MA0162.11.26636
MA0163.10.116706
MA0164.10.600609
MA0080.20.908823
MA0018.20.610433
MA0099.20.721008
MA0079.20.323753
MA0102.21.65195
MA0258.10.246285
MA0259.10.729797
MA0442.10
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