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MCL coexpression mm9:1163: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0010314!5.38e-23!92;UBERON:0000073!7.35e-17!54;UBERON:0001017!8.01e-17!73;UBERON:0001016!2.22e-16!75;UBERON:0002346!2.64e-16!64;UBERON:0003075!2.64e-16!64;UBERON:0007284!2.64e-16!64;UBERON:0001049!1.29e-15!52;UBERON:0005068!1.29e-15!52;UBERON:0006241!1.29e-15!52;UBERON:0007135!1.29e-15!52;UBERON:0004121!3.15e-15!95;UBERON:0000924!3.15e-15!95;UBERON:0006601!3.15e-15!95;UBERON:0010371!2.26e-14!73;UBERON:0002020!2.05e-13!34;UBERON:0000955!7.49e-13!47;UBERON:0006238!7.49e-13!47;UBERON:0002616!1.75e-12!46;UBERON:0003056!4.82e-11!49;UBERON:0003528!6.42e-11!29;UBERON:0002791!6.42e-11!29;UBERON:0001893!6.42e-11!29;UBERON:0003080!1.56e-10!40;UBERON:0004111!5.09e-10!122;UBERON:0002780!5.93e-10!39;UBERON:0001890!5.93e-10!39;UBERON:0006240!5.93e-10!39;UBERON:0000025!1.59e-09!114;UBERON:0000468!5.58e-08!333;UBERON:0000956!8.78e-08!21;UBERON:0001869!8.78e-08!21;UBERON:0000203!8.78e-08!21;UBERON:0002619!6.73e-07!17
|tfbs_overrepresentation_for_novel_motifs=0.438063,1.45672,0.411716,1.20801,0.299217,0.495263,0.587291,0.206208,0.616096,0.826837,1.34037,0.575086,0.206435,0.599731,0.315771,0,0.795315,0.291368,0.19222,0.112498,0.374752,0.27937,0.598814,0.29769,0.419327,0.62766,0.184473,0.516511,2.46776,1.41139,0.50223,0.897561,0.78719,0.166577,0.316253,1.51308,1.40094,0.57142,0.258564,0.230656,0.295233,0.507468,0.0742755,0.317766,0.822425,0.469348,0.714592,1.31862,0.219744,0.347313,0.777641,0.654933,0.139618,1.04034,1.0579,0.606984,0.356236,0.56214,0.522357,0.604914,2.03558,0.664501,0.226529,0.766235,1.49952,0.807219,1.19497,1.54543,0.872612,1.39786,1.01778,0.608073,0.611537,1.09164,1.55661,0.936963,0.166511,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,0.200155,0.975495,0.613286,0.042613,0.145788,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,1.30733,0.237542,0.203879,0.913319,0.71485,0.127063,0.280055,0.897279,1.02279,0.778243,1.82972,1.26443,0.837607,0.528416,2.65673,0.982279,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,2.11126,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,2.81475,1.32639,0.863723,0.595563,0.903645,1.19345,0.829907,1.00568,1.19218,1.16374,0.620831,1.29374,0.580299,1.13474,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,1.81619,0.507927,0.717753,2.03691,0.448938,0.813943,0.147909,4.59664,1.04192,1.26486,0.619892,1.12411,0.655955,0.327731,1.94562,0.446272,1.25393,0.974632,0.864173,1.09603,0.767269,0.612377,1.3969,0.573477,1.86859
}}

Latest revision as of 16:29, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr18:23573663..23573716,+p7@Dtna
Mm9::chr19:7062081..7062108,-p3@Vegfb
Mm9::chr1:74331613..74331646,+p1@Pnkd
Mm9::chr3:127201904..127201956,-p1@Gm4392
Mm9::chr3:127201967..127201989,-p7@Ank2
Mm9::chr3:127201994..127202011,-p13@Ank2
Mm9::chr3:127202013..127202055,-p10@Ank2


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:0016014dystrobrevin complex0.0177505067660111



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
CNS neuron (sensu Vertebrata)3.62e-0923
neuroblast (sensu Vertebrata)3.62e-0923
neuron6.49e-0833
neuronal stem cell6.49e-0833
neuroblast6.49e-0833
electrically signaling cell6.49e-0833

Uber Anatomy
Ontology termp-valuen
structure with developmental contribution from neural crest5.38e-2392
regional part of nervous system7.35e-1754
central nervous system8.01e-1773
nervous system2.22e-1675
neurectoderm2.64e-1664
neural plate2.64e-1664
presumptive neural plate2.64e-1664
neural tube1.29e-1552
neural rod1.29e-1552
future spinal cord1.29e-1552
neural keel1.29e-1552
ectoderm-derived structure3.15e-1595
ectoderm3.15e-1595
presumptive ectoderm3.15e-1595
ecto-epithelium2.26e-1473
gray matter2.05e-1334
brain7.49e-1347
future brain7.49e-1347
regional part of brain1.75e-1246
pre-chordal neural plate4.82e-1149
brain grey matter6.42e-1129
regional part of telencephalon6.42e-1129
telencephalon6.42e-1129
anterior neural tube1.56e-1040
anatomical conduit5.09e-10122
regional part of forebrain5.93e-1039
forebrain5.93e-1039
future forebrain5.93e-1039
tube1.59e-09114
multi-cellular organism5.58e-08333
cerebral cortex8.78e-0821
cerebral hemisphere8.78e-0821
pallium8.78e-0821
regional part of cerebral cortex6.73e-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
MA0006.10.837454
MA0007.10.465969
MA0009.10.92425
MA0014.18.22991
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
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.11.8892
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.14.34044
MA0056.10
MA0057.10.376102
MA0058.10.384683
MA0059.10.397033
MA0060.10.656954
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
MA0073.11.3018
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
MA0092.11.13539
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.488671
MA0106.12.73793
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
MA0119.11.04809
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
MA0141.10.368264
MA0142.10.814115
MA0143.11.59922
MA0144.10.262477
MA0145.10.0910975
MA0146.11.15352
MA0147.11.38091
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.22.09945
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.22.57676
MA0047.20.626803
MA0112.20.631649
MA0065.21.56466
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
MA0160.11.25065
MA0161.10
MA0162.12.75316
MA0163.13.21163
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.21.47363
MA0102.21.65195
MA0258.10.246285
MA0259.10.26402
MA0442.10
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