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MCL coexpression mm9:1022: Difference between revisions

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{{MCL_coexpression_mm9
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oxidase activity;0.0173986206403512;70503!GO:0008445;D-aspartate oxidase activity;0.0173986206403512;70503!GO:0003884;D-amino-acid oxidase activity;0.0173986206403512;70503!GO:0006531;aspartate metabolic process;0.0173986206403512;70503!GO:0044444;cytoplasmic part;0.0173986206403512;240667,18604,70772,107227,70503!GO:0006086;acetyl-CoA biosynthetic process from pyruvate;0.0194060622428501;18604!GO:0004740;pyruvate dehydrogenase (acetyl-transferring) kinase activity;0.0194060622428501;18604!GO:0007320;insemination;0.0194060622428501;70503!GO:0018106;peptidyl-histidine phosphorylation;0.0194060622428501;18604!GO:0007620;copulation;0.0194060622428501;70503!GO:0006085;acetyl-CoA biosynthetic process;0.0194060622428501;18604!GO:0018202;peptidyl-histidine modification;0.0194060622428501;18604!GO:0007625;grooming behavior;0.0194060622428501;70503!GO:0004673;protein histidine kinase activity;0.0300167411853002;18604!GO:0007618;mating;0.0345885816586775;70503!GO:0009066;aspartate family amino acid metabolic process;0.0345885816586775;70503!GO:0016775;phosphotransferase activity, nitrogenous group as acceptor;0.0345885816586775;18604!GO:0016641;oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor;0.037323481861197;70503!GO:0016638;oxidoreductase activity, acting on the CH-NH2 group of donors;0.0440581817269506;70503!GO:0006090;pyruvate metabolic process;0.0440581817269506;18604!GO:0000003;reproduction;0.0454201494827825;70772,70503!GO:0019752;carboxylic acid metabolic process;0.046996765005203;18604,70503!GO:0006082;organic acid metabolic 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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003914!2.02e-09!47;UBERON:0000468!3.86e-07!333;UBERON:0007100!4.85e-07!18;UBERON:0000948!4.85e-07!18;UBERON:0005498!4.85e-07!18;UBERON:0004140!4.85e-07!18;UBERON:0009881!4.85e-07!18;UBERON:0004141!4.85e-07!18;UBERON:0003084!4.85e-07!18;UBERON:0007005!4.85e-07!18;UBERON:0004139!4.85e-07!18;UBERON:0004291!4.85e-07!18
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.0418382,0.411716,0.480627,0.299217,0.495263,0.587291,0.594722,0.215218,0.826837,0.542749,0.575086,0.206435,0.599731,0.847296,0,0.795315,0.291368,0.19222,0.361892,0.374752,0.586604,0.598814,0.80655,0.419327,0.62766,0.184473,0.516511,2.46776,0.876948,0.50223,0.897561,0.289148,0.498917,1.53201,0.0235321,0.766323,2.39515,0.258564,0.230656,0.295233,0.507468,0.258106,0.851774,0.115244,0.469348,0.714592,0.532496,0.219744,0.917701,0.777641,1.57618,0.431711,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,1.01778,0.21183,0.293368,1.09164,3.7644,0.936963,0.498755,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,0.200155,0.975495,0.146394,0.374181,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,0.589174,0.913319,0.71485,0.399703,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.998363,0.376549,0.430942,1.02459,1.75621,0.547992,1.27206,0.293461,1.59063,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,1.45183,2.08944,1.19345,0.308038,1.00568,2.07207,1.16374,0.620831,1.29374,0.979575,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.813943,0.452587,0.256263,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,0.435579,1.13413,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,0.705627
|tfbs_overrepresentation_jaspar=MA0003.1;0.79075,MA0004.1;1.20906,MA0006.1;0.837454,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;1.02494,MA0017.1;3.35545,MA0019.1;1.753,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;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;1.0092,MA0056.1;0,MA0057.1;0.117936,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;0.232592,MA0061.1;0.724575,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;0.00223012,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;1.49527,MA0089.1;0,MA0090.1;0.446539,MA0091.1;0.494398,MA0092.1;1.13539,MA0093.1;0.879104,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;0.406019,MA0103.1;0.920496,MA0105.1;1.5116,MA0106.1;0.677988,MA0107.1;1.62481,MA0108.2;0.763162,MA0109.1;0,MA0111.1;0.460823,MA0113.1;0.649407,MA0114.1;1.32534,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;0.964041,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.262477,MA0145.1;1.56174,MA0146.1;0.264322,MA0147.1;0.753844,MA0148.1;2.15276,MA0149.1;0.411562,MA0062.2;0.167299,MA0035.2;0.573016,MA0039.2;0.219063,MA0138.2;0.727395,MA0002.2;0.592533,MA0137.2;0.365364,MA0104.2;0.624968,MA0047.2;0.626803,MA0112.2;1.05549,MA0065.2;1.0577,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.792589,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;0.302441,MA0163.1;0.0280055,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;0.00878868,MA0102.2;1.65195,MA0258.1;1.27611,MA0259.1;1.34223,MA0442.1;0
}}

Latest revision as of 16:16, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:40349793..40349859,+p1@Ddo
Mm9::chr11:94901820..94901857,-p7@Pdk2
Mm9::chr17:27154950..27155012,+p2@Ggnbp1
Mm9::chr19:44620299..44620322,-p2@Sec31b
Mm9::chr19:44620326..44620361,-p1@Sec31b
Mm9::chr19:7131357..7131423,+p1@Macrod1
Mm9::chr4:33276385..33276430,-p1@Pm20d2


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:0015922aspartate oxidase activity0.0173986206403512
GO:0008445D-aspartate oxidase activity0.0173986206403512
GO:0003884D-amino-acid oxidase activity0.0173986206403512
GO:0006531aspartate metabolic process0.0173986206403512
GO:0044444cytoplasmic part0.0173986206403512
GO:0006086acetyl-CoA biosynthetic process from pyruvate0.0194060622428501
GO:0004740pyruvate dehydrogenase (acetyl-transferring) kinase activity0.0194060622428501
GO:0007320insemination0.0194060622428501
GO:0018106peptidyl-histidine phosphorylation0.0194060622428501
GO:0007620copulation0.0194060622428501
GO:0006085acetyl-CoA biosynthetic process0.0194060622428501
GO:0018202peptidyl-histidine modification0.0194060622428501
GO:0007625grooming behavior0.0194060622428501
GO:0004673protein histidine kinase activity0.0300167411853002
GO:0007618mating0.0345885816586775
GO:0009066aspartate family amino acid metabolic process0.0345885816586775
GO:0016775phosphotransferase activity, nitrogenous group as acceptor0.0345885816586775
GO:0016641oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor0.037323481861197
GO:0016638oxidoreductase activity, acting on the CH-NH2 group of donors0.0440581817269506
GO:0006090pyruvate metabolic process0.0440581817269506
GO:0000003reproduction0.0454201494827825
GO:0019752carboxylic acid metabolic process0.046996765005203
GO:0006082organic acid metabolic process0.046996765005203



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
epithelial tube2.02e-0947
multi-cellular organism3.86e-07333
primary circulatory organ4.85e-0718
heart4.85e-0718
primitive heart tube4.85e-0718
primary heart field4.85e-0718
anterior lateral plate mesoderm4.85e-0718
heart tube4.85e-0718
heart primordium4.85e-0718
cardiac mesoderm4.85e-0718
cardiogenic plate4.85e-0718
heart rudiment4.85e-0718


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)
MA0003.10.79075
MA0004.11.20906
MA0006.10.837454
MA0007.10.465969
MA0009.10.92425
MA0014.11.02494
MA0017.13.35545
MA0019.11.753
MA0024.10.880057
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
MA0055.11.0092
MA0056.10
MA0057.10.117936
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.10.724575
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.121435
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.00223012
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.11.49527
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.11.13539
MA0093.10.879104
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.920496
MA0105.11.5116
MA0106.10.677988
MA0107.11.62481
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.11.32534
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
MA0141.10.964041
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.11.56174
MA0146.10.264322
MA0147.10.753844
MA0148.12.15276
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.20.219063
MA0138.20.727395
MA0002.20.592533
MA0137.20.365364
MA0104.20.624968
MA0047.20.626803
MA0112.21.05549
MA0065.21.0577
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.792589
MA0155.10.687925
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.10.302441
MA0163.10.0280055
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.20.00878868
MA0102.21.65195
MA0258.11.27611
MA0259.11.34223
MA0442.10
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