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MCL coexpression mm9:1086: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0004602;glutathione peroxidase activity;0.037899835520948;14776!GO:0008430;selenium binding;0.037899835520948;14776!GO:0004601;peroxidase activity;0.037899835520948;14776!GO:0016684;oxidoreductase activity, acting on peroxide as acceptor;0.037899835520948;14776!GO:0006979;response to oxidative stress;0.0413180817439719;14776!
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|ontology_enrichment_uberon=UBERON:0000160!5.63e-23!31;UBERON:0005409!6.53e-23!47;UBERON:0001007!5.09e-16!116;UBERON:0001555!5.09e-16!116;UBERON:0007026!5.09e-16!116;UBERON:0004119!6.80e-16!118;UBERON:0000925!6.80e-16!118;UBERON:0006595!6.80e-16!118;UBERON:0004921!1.03e-14!114;UBERON:0000344!3.66e-13!15;UBERON:0001242!1.75e-11!13;UBERON:0000060!1.75e-11!13;UBERON:0001262!1.75e-11!13;UBERON:0004786!1.75e-11!13;UBERON:0000485!8.26e-09!11;UBERON:0005178!1.45e-08!17;UBERON:0005181!1.45e-08!17;UBERON:0002224!1.45e-08!17;UBERON:0000915!1.45e-08!17;UBERON:0008947!1.45e-08!17;UBERON:0003258!1.45e-08!17;UBERON:0003350!2.56e-08!9;UBERON:0004808!2.56e-08!9;UBERON:0001277!2.56e-08!9;UBERON:0004923!3.55e-07!24;UBERON:0005153!4.20e-07!17
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.0418382,0.411716,0.480627,0.299217,0.495263,0.587291,0.594722,0.616096,0.478312,0.542749,0.575086,1.12363,0.599731,0.315771,0,0.795315,0.291368,0.19222,0.361892,0.374752,0.08187,0.598814,0.29769,0.419327,0.62766,0.542568,0.516511,0.344372,0.876948,0.50223,0.897561,1.43437,0.498917,0.316253,0.756613,0.279977,0.57142,0.717242,0.652422,0.295233,0.507468,0.258106,0.317766,0.515031,0.469348,0.714592,0.532496,0.219744,0.347313,0.777641,0.654933,0.431711,1.04034,1.0579,0.606984,0.356236,1.3814,0.522357,0.604914,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.21183,0.0869413,1.09164,0.17012,0.159969,0.166511,0.703064,0.859987,0.378988,1.79723,0.812889,0.663039,0.200155,0.975495,0.339494,0.164297,0.447265,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,0.203879,0.913319,0.71485,0.127063,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,1.10097,1.02459,0.380122,0.547992,1.27206,0.293461,0.418498,1.21618,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,1.98263,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,1.26636,0.717753,2.03691,0.448938,0.300961,0.147909,0.256263,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,0.435579,1.13413,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,0.278874,0.573477,1.86859
|tfbs_overrepresentation_jaspar=MA0003.1;1.4232,MA0004.1;0.481116,MA0006.1;0.311391,MA0007.1;1.17655,MA0009.1;0.92425,MA0014.1;0.694761,MA0017.1;3.35545,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;0.62758,MA0040.1;0.936879,MA0041.1;0.404721,MA0042.1;0.391504,MA0043.1;1.02178,MA0046.1;0.960497,MA0048.1;1.30252,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;0.384683,MA0059.1;0.397033,MA0060.1;0.232592,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;2.22537,MA0072.1;0.927016,MA0073.1;0.046559,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;0.285759,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;1.64639,MA0105.1;1.5116,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;0.719313,MA0115.1;1.0246,MA0116.1;6.25316,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;0.585936,MA0140.1;0.568252,MA0141.1;0.964041,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.262477,MA0145.1;0.0910975,MA0146.1;2.04073,MA0147.1;0.274511,MA0148.1;0.49752,MA0149.1;4.89552,MA0062.2;1.54019,MA0035.2;0.573016,MA0039.2;5.54084,MA0138.2;0.727395,MA0002.2;0.592533,MA0137.2;0.365364,MA0104.2;0.624968,MA0047.2;0.626803,MA0112.2;0.304722,MA0065.2;0.633155,MA0150.1;2.04738,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;1.87278,MA0155.1;0.336768,MA0156.1;0.356017,MA0157.1;0.781683,MA0158.1;0,MA0159.1;4.92444,MA0160.1;1.25065,MA0161.1;0,MA0162.1;0.127623,MA0163.1;1.63182,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;1.05304,MA0102.2;1.65195,MA0258.1;0.688848,MA0259.1;0.26402,MA0442.1;0
}}

Latest revision as of 16:22, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:69779098..69779123,+p4@Cldn7
Mm9::chr12:77896412..77896451,-p1@Gpx2
Mm9::chr12:77896458..77896465,-p3@Gpx2
Mm9::chr12:77896476..77896508,-p2@Gpx2
Mm9::chr5:31554051..31554101,+p1@Krtcap3
Mm9::chr5:31554116..31554131,+p2@Krtcap3
Mm9::chr5:31554284..31554295,+p3@Krtcap3


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:0004602glutathione peroxidase activity0.037899835520948
GO:0008430selenium binding0.037899835520948
GO:0004601peroxidase activity0.037899835520948
GO:0016684oxidoreductase activity, acting on peroxide as acceptor0.037899835520948
GO:0006979response to oxidative stress0.0413180817439719



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>

Cell Type
Ontology termp-valuen
intestinal epithelial cell2.56e-089
epithelial cell of alimentary canal2.56e-089
epithelial cell6.06e-0825
endo-epithelial cell1.36e-0715

Uber Anatomy
Ontology termp-valuen
intestine5.63e-2331
gastrointestinal system6.53e-2347
digestive system5.09e-16116
digestive tract5.09e-16116
primitive gut5.09e-16116
endoderm-derived structure6.80e-16118
endoderm6.80e-16118
presumptive endoderm6.80e-16118
subdivision of digestive tract1.03e-14114
mucosa3.66e-1315
intestinal mucosa1.75e-1113
anatomical wall1.75e-1113
wall of intestine1.75e-1113
gastrointestinal system mucosa1.75e-1113
simple columnar epithelium8.26e-0911
thoracic cavity element1.45e-0817
thoracic segment organ1.45e-0817
thoracic cavity1.45e-0817
thoracic segment of trunk1.45e-0817
respiratory primordium1.45e-0817
endoderm of foregut1.45e-0817
epithelium of mucosa2.56e-089
gastrointestinal system epithelium2.56e-089
intestinal epithelium2.56e-089
organ component layer3.55e-0724
epithelial bud4.20e-0717


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)
MA0003.11.4232
MA0004.10.481116
MA0006.10.311391
MA0007.11.17655
MA0009.10.92425
MA0014.10.694761
MA0017.13.35545
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.321735
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.11.30252
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.362005
MA0056.10
MA0057.10.376102
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.10.261749
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.121435
MA0069.10.945354
MA0070.10.93557
MA0071.12.22537
MA0072.10.927016
MA0073.10.046559
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.285759
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.11.64639
MA0105.11.5116
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.719313
MA0115.11.0246
MA0116.16.25316
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
MA0139.10.585936
MA0140.10.568252
MA0141.10.964041
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.0910975
MA0146.12.04073
MA0147.10.274511
MA0148.10.49752
MA0149.14.89552
MA0062.21.54019
MA0035.20.573016
MA0039.25.54084
MA0138.20.727395
MA0002.20.592533
MA0137.20.365364
MA0104.20.624968
MA0047.20.626803
MA0112.20.304722
MA0065.20.633155
MA0150.12.04738
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.11.87278
MA0155.10.336768
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.14.92444
MA0160.11.25065
MA0161.10
MA0162.10.127623
MA0163.11.63182
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.21.05304
MA0102.21.65195
MA0258.10.688848
MA0259.10.26402
MA0442.10
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