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MCL coexpression mm9:1091: Difference between revisions

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{{MCL_coexpression_mm9
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esis;0.0120815599975684;217039,23885!GO:0048232;male 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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000160!3.35e-08!31;UBERON:0004119!8.33e-07!118;UBERON:0000925!8.33e-07!118;UBERON:0006595!8.33e-07!118
|tfbs_overrepresentation_for_novel_motifs=1.11639,0.369498,1.86463,0.480627,0.299217,0.495263,0.587291,0.206208,0.215218,1.25386,0.542749,0.575086,0.206435,0.599731,0.315771,0,1.86712,0.291368,0.561256,0.112498,0.374752,0.27937,0.598814,0.29769,1.07577,0.62766,0.542568,0.516511,1.63164,0.446946,0.50223,0.897561,0.289148,0.498917,0.848378,0.468714,2.14888,0.57142,0.258564,0.230656,0.295233,1.26538,0.0742755,0.317766,0.515031,1.18381,0.714592,0.532496,0.219744,0.347313,0.777641,1.57618,0.139618,1.04034,1.0579,2.51033,0.356236,0.56214,0.176152,1.47148,0.877332,0.664501,0.226529,0.766235,1.49952,0.807219,1.19497,1.54543,0.872612,1.39786,1.01778,0.21183,1.02583,1.09164,1.55661,0.936963,0.166511,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,0.200155,0.975495,0.960306,0.374181,0.447265,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.668513,0.203879,0.913319,0.71485,1.29592,0.280055,0.897279,1.02279,0.778243,0.777175,3.22326,0.837607,0.528416,0.998363,1.74385,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,3.97128,0.484437,0.796633,0.276329,1.09707,1.76329,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,2.67845,0.308038,1.00568,0.473246,1.16374,1.50487,1.29374,0.275843,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,2.25449,0.147909,0.545091,1.04192,0.681896,0.619892,1.12411,0.655955,0.327731,0.435579,4.00677,1.25393,0.974632,0.864173,1.92222,0.767269,0.612377,0.278874,0.573477,0.705627
|tfbs_overrepresentation_jaspar=MA0003.1;1.08574,MA0004.1;0.481116,MA0006.1;0.837454,MA0007.1;1.17655,MA0009.1;0.92425,MA0014.1;1.84673,MA0017.1;0.337808,MA0019.1;0.740036,MA0024.1;0.880057,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;1.519,MA0040.1;0.936879,MA0041.1;0.404721,MA0042.1;0.391504,MA0043.1;1.02178,MA0046.1;0.960497,MA0048.1;4.87424,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;6.55067,MA0056.1;0,MA0057.1;0.756125,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;1.90283,MA0061.1;2.05557,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;40.9137,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;0.598004,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;1.39455,MA0101.1;0.406019,MA0103.1;0.348572,MA0105.1;1.5116,MA0106.1;0.677988,MA0107.1;0.906859,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;0.735438,MA0132.1;0,MA0133.1;0,MA0135.1;1.05845,MA0136.1;0.600242,MA0139.1;0.202522,MA0140.1;1.3943,MA0141.1;0.368264,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.262477,MA0145.1;2.13876,MA0146.1;1.57153,MA0147.1;0.274511,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.967192,MA0035.2;0.573016,MA0039.2;2.51018,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;0.957645,MA0104.2;0.624968,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;0.356017,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.284457,MA0160.1;0.50056,MA0161.1;0,MA0162.1;1.71182,MA0163.1;1.20194,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;13.7759,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;0.729797,MA0442.1;0
}}

Latest revision as of 16:22, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:84683533..84683609,-p2@Ggnbp2
Mm9::chr11:84683630..84683684,-p3@Ggnbp2
Mm9::chr11:84684214..84684309,-p1@Ggnbp2
Mm9::chr19:46227013..46227056,+p1@Gbf1
Mm9::chr1:192752380..192752429,+p2@Angel2
Mm9::chr6:86683262..86683388,-p1@Gmcl1
Mm9::chr6:97129094..97129153,-p1@Tmf1


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:0007283spermatogenesis0.0120815599975684
GO:0048232male gamete generation0.0120815599975684
GO:0050220prostaglandin-E synthase activity0.0120815599975684
GO:0007276gamete generation0.0120815599975684
GO:0019953sexual reproduction0.013172754452041
GO:0015035protein disulfide oxidoreductase activity0.0142935359858534
GO:0046457prostanoid biosynthetic process0.0142935359858534
GO:0001516prostaglandin biosynthetic process0.0142935359858534
GO:0000003reproduction0.0150846207950959
GO:0006693prostaglandin metabolic process0.0154804218436046
GO:0006692prostanoid metabolic process0.0154804218436046
GO:0015036disulfide oxidoreductase activity0.0154804218436046
GO:0016363nuclear matrix0.0164862161938072
GO:0046456icosanoid biosynthetic process0.0244817277806222
GO:0006690icosanoid metabolic process0.0285526234360812
GO:0045454cell redox homeostasis0.0360849429900489
GO:0016860intramolecular oxidoreductase activity0.0360849429900489
GO:0005634nucleus0.0483232202533136
GO:0006633fatty acid biosynthetic process0.0495102897600699
GO:0016053organic acid biosynthetic process0.0495102897600699
GO:0046394carboxylic acid biosynthetic process0.0495102897600699



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
intestine3.35e-0831
endoderm-derived structure8.33e-07118
endoderm8.33e-07118
presumptive endoderm8.33e-07118


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)
MA0003.11.08574
MA0004.10.481116
MA0006.10.837454
MA0007.11.17655
MA0009.10.92425
MA0014.11.84673
MA0017.10.337808
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.321735
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.11.519
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.14.87424
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.16.55067
MA0056.10
MA0057.10.756125
MA0058.10.384683
MA0059.10.397033
MA0060.11.90283
MA0061.12.05557
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.121435
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.140.9137
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.598004
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.11.39455
MA0101.10.406019
MA0103.10.348572
MA0105.11.5116
MA0106.10.677988
MA0107.10.906859
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
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.10.202522
MA0140.11.3943
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.12.13876
MA0146.11.57153
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.20.967192
MA0035.20.573016
MA0039.22.51018
MA0138.20.727395
MA0002.20.205289
MA0137.20.957645
MA0104.20.624968
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
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.11.71182
MA0163.11.20194
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.213.7759
MA0102.21.65195
MA0258.10.246285
MA0259.10.729797
MA0442.10
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