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MCL coexpression mm9:1097: Difference between revisions

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{{MCL_coexpression_mm9
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replication;0.000130837892876762;23834,12447!GO:0022402;cell cycle process;0.00408491639531306;23834,12447,17865!GO:0006259;DNA metabolic process;0.00408491639531306;23834,12447!GO:0007049;cell cycle;0.0045787611389747;23834,12447,17865!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0112369554901173;23834,12447,17865!GO:0051301;cell division;0.0136759545366786;23834,12447!GO:0000307;cyclin-dependent protein kinase holoenzyme complex;0.0186178917305763;12447!GO:0051726;regulation of cell cycle;0.0203336441198166;12447,17865!GO:0005634;nucleus;0.0203336441198166;23834,12447,17865!GO:0043283;biopolymer metabolic process;0.0206797517638527;23834,12447,17865!GO:0006270;DNA replication initiation;0.0220079684496529;12447!GO:0017111;nucleoside-triphosphatase activity;0.0220079684496529;23834!GO:0016462;pyrophosphatase activity;0.0220079684496529;23834!GO:0016818;hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides;0.0220079684496529;23834!GO:0016817;hydrolase activity, acting on acid anhydrides;0.0220079684496529;23834!GO:0016538;cyclin-dependent protein kinase regulator activity;0.024407879672774;12447!GO:0043170;macromolecule metabolic process;0.0362424271274993;23834,12447,17865!GO:0005819;spindle;0.0392044077488713;23834!GO:0006261;DNA-dependent DNA replication;0.044930617520457;12447!GO:0044238;primary metabolic process;0.0486474848363971;23834,12447,17865!GO:0044237;cellular metabolic process;0.0486474848363971;23834,12447,17865!GO:0043231;intracellular membrane-bound organelle;0.0486474848363971;23834,12447,17865!GO:0043227;membrane-bound organelle;0.0486474848363971;23834,12447,17865!GO:0019887;protein kinase regulator 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|gostat_on_MCL_coexpression=GO:0006260;DNA replication;0.000130837892876762;23834,12447!GO:0022402;cell cycle process;0.00408491639531306;23834,12447,17865!GO:0006259;DNA metabolic process;0.00408491639531306;23834,12447!GO:0007049;cell cycle;0.0045787611389747;23834,12447,17865!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0112369554901173;23834,12447,17865!GO:0051301;cell division;0.0136759545366786;23834,12447!GO:0000307;cyclin-dependent protein kinase holoenzyme complex;0.0186178917305763;12447!GO:0051726;regulation of cell cycle;0.0203336441198166;12447,17865!GO:0005634;nucleus;0.0203336441198166;23834,12447,17865!GO:0043283;biopolymer metabolic process;0.0206797517638527;23834,12447,17865!GO:0006270;DNA replication initiation;0.0220079684496529;12447!GO:0017111;nucleoside-triphosphatase activity;0.0220079684496529;23834!GO:0016462;pyrophosphatase activity;0.0220079684496529;23834!GO:0016818;hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides;0.0220079684496529;23834!GO:0016817;hydrolase activity, acting on acid anhydrides;0.0220079684496529;23834!GO:0016538;cyclin-dependent protein kinase regulator activity;0.024407879672774;12447!GO:0043170;macromolecule metabolic process;0.0362424271274993;23834,12447,17865!GO:0005819;spindle;0.0392044077488713;23834!GO:0006261;DNA-dependent DNA replication;0.044930617520457;12447!GO:0044238;primary metabolic process;0.0486474848363971;23834,12447,17865!GO:0044237;cellular metabolic process;0.0486474848363971;23834,12447,17865!GO:0043231;intracellular membrane-bound organelle;0.0486474848363971;23834,12447,17865!GO:0043227;membrane-bound organelle;0.0486474848363971;23834,12447,17865!GO:0019887;protein kinase regulator activity;0.0486474848363971;12447!
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.369498,1.05921,0.480627,0.299217,0.495263,0.587291,0.206208,0.215218,2.30523,0.542749,0.575086,0.59526,0.599731,0.847296,0,0.795315,0.291368,0.19222,0.361892,0.374752,0.586604,0.598814,0.29769,1.07577,0.62766,0.542568,0.516511,0.344372,0.145661,1.25421,0.897561,1.43437,0.166577,1.53201,0.0235321,2.98785,0.57142,0.717242,0.652422,0.295233,0.507468,0.0742755,0.317766,0.822425,0.469348,0.714592,0.532496,0.219744,0.347313,0.777641,0.654933,0.851157,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,4.21144,3.39997,1.09164,4.62315,0.936963,0.498755,0.703064,0.859987,0.378988,0.610783,0.812889,0.663039,1.72681,0.975495,4.20174,0.374181,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.668513,0.203879,0.913319,0.71485,0.127063,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,1.35148,1.27206,0.293461,2.68499,1.21618,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,1.45183,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.979575,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.452587,4.59664,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,0.435579,1.13413,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,2.35446
|tfbs_overrepresentation_jaspar=MA0003.1;6.59917,MA0004.1;0.481116,MA0006.1;0.311391,MA0007.1;3.03758,MA0009.1;0.92425,MA0014.1;1.02494,MA0017.1;0.337808,MA0019.1;0.740036,MA0024.1;2.04116,MA0025.1;1.15921,MA0027.1;2.57545,MA0028.1;0.321735,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;2.45917,MA0056.1;0,MA0057.1;0.117936,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;0.656954,MA0061.1;0.261749,MA0063.1;0,MA0066.1;0.616444,MA0067.1;1.27078,MA0068.1;0.385183,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;0.519509,MA0072.1;0.927016,MA0073.1;0.00223012,MA0074.1;0.580087,MA0076.1;0.356883,MA0077.1;0.905143,MA0078.1;0.670113,MA0081.1;0.420276,MA0083.1;1.02098,MA0084.1;1.59945,MA0087.1;0.977537,MA0088.1;1.00582,MA0089.1;0,MA0090.1;0.446539,MA0091.1;0.494398,MA0092.1;0.446857,MA0093.1;0.329976,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;0.406019,MA0103.1;0.348572,MA0105.1;0.162418,MA0106.1;1.62423,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;2.30533,MA0117.1;3.71996,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;0.202522,MA0140.1;0.568252,MA0141.1;0.368264,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.262477,MA0145.1;1.05551,MA0146.1;3.71137,MA0147.1;0.753844,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.500692,MA0035.2;0.573016,MA0039.2;9.35346,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;0.957645,MA0104.2;1.17226,MA0047.2;0.626803,MA0112.2;0.631649,MA0065.2;0.633155,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;1.29007,MA0155.1;0.687925,MA0156.1;0.356017,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.284457,MA0160.1;0.50056,MA0161.1;0,MA0162.1;2.20906,MA0163.1;1.20194,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;1.96358,MA0102.2;1.65195,MA0258.1;0.688848,MA0259.1;1.34223,MA0442.1;0
}}

Latest revision as of 16:23, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:98769124..98769138,+p2@Cdc6
Mm9::chr2:162880327..162880385,+p2@Mybl2
Mm9::chr2:162880387..162880413,+p1@Mybl2
Mm9::chr2:162880418..162880429,+p4@Mybl2
Mm9::chr4:108252086..108252094,+p2@Orc1
Mm9::chr7:38892471..38892504,-p1@Ccne1
Mm9::chr7:38892509..38892528,-p2@Ccne1


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:0006260DNA replication0.000130837892876762
GO:0022402cell cycle process0.00408491639531306
GO:0006259DNA metabolic process0.00408491639531306
GO:0007049cell cycle0.0045787611389747
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0112369554901173
GO:0051301cell division0.0136759545366786
GO:0000307cyclin-dependent protein kinase holoenzyme complex0.0186178917305763
GO:0051726regulation of cell cycle0.0203336441198166
GO:0005634nucleus0.0203336441198166
GO:0043283biopolymer metabolic process0.0206797517638527
GO:0006270DNA replication initiation0.0220079684496529
GO:0017111nucleoside-triphosphatase activity0.0220079684496529
GO:0016462pyrophosphatase activity0.0220079684496529
GO:0016818hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides0.0220079684496529
GO:0016817hydrolase activity, acting on acid anhydrides0.0220079684496529
GO:0016538cyclin-dependent protein kinase regulator activity0.024407879672774
GO:0043170macromolecule metabolic process0.0362424271274993
GO:0005819spindle0.0392044077488713
GO:0006261DNA-dependent DNA replication0.044930617520457
GO:0044238primary metabolic process0.0486474848363971
GO:0044237cellular metabolic process0.0486474848363971
GO:0043231intracellular membrane-bound organelle0.0486474848363971
GO:0043227membrane-bound organelle0.0486474848363971
GO:0019887protein kinase regulator activity0.0486474848363971



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)
MA0003.16.59917
MA0004.10.481116
MA0006.10.311391
MA0007.13.03758
MA0009.10.92425
MA0014.11.02494
MA0017.10.337808
MA0019.10.740036
MA0024.12.04116
MA0025.11.15921
MA0027.12.57545
MA0028.10.321735
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
MA0055.12.45917
MA0056.10
MA0057.10.117936
MA0058.10.384683
MA0059.10.397033
MA0060.10.656954
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.385183
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.00223012
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.11.00582
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.162418
MA0106.11.62423
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.259463
MA0115.11.0246
MA0116.12.30533
MA0117.13.71996
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
MA0139.10.202522
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.11.05551
MA0146.13.71137
MA0147.10.753844
MA0148.10.49752
MA0149.10.411562
MA0062.20.500692
MA0035.20.573016
MA0039.29.35346
MA0138.20.727395
MA0002.20.205289
MA0137.20.957645
MA0104.21.17226
MA0047.20.626803
MA0112.20.631649
MA0065.20.633155
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.11.29007
MA0155.10.687925
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.12.20906
MA0163.11.20194
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.21.96358
MA0102.21.65195
MA0258.10.688848
MA0259.11.34223
MA0442.10
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