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|ontology_enrichment_uberon=UBERON:0010371!3.55e-22!73;UBERON:0004121!6.22e-22!95;UBERON:0000924!6.22e-22!95;UBERON:0006601!6.22e-22!95;UBERON:0002346!5.40e-20!64;UBERON:0003075!5.40e-20!64;UBERON:0007284!5.40e-20!64;UBERON:0000073!1.13e-18!54;UBERON:0001017!1.66e-17!73;UBERON:0001016!2.56e-17!75;UBERON:0001049!3.76e-17!52;UBERON:0005068!3.76e-17!52;UBERON:0006241!3.76e-17!52;UBERON:0007135!3.76e-17!52;UBERON:0003056!7.59e-16!49;UBERON:0000955!2.69e-14!47;UBERON:0006238!2.69e-14!47;UBERON:0002616!1.28e-13!46;UBERON:0010314!4.83e-13!92;UBERON:0003080!1.41e-12!40;UBERON:0002020!1.55e-12!34;UBERON:0002780!6.43e-12!39;UBERON:0001890!6.43e-12!39;UBERON:0006240!6.43e-12!39;UBERON:0003528!8.74e-10!29;UBERON:0002791!8.74e-10!29;UBERON:0001893!8.74e-10!29;UBERON:0000489!2.60e-07!21;UBERON:0002619!2.96e-07!17;UBERON:0002021!3.89e-07!10;UBERON:0000411!3.89e-07!10;UBERON:0001950!3.89e-07!10
|ontology_enrichment_uberon=UBERON:0010371!3.55e-22!73;UBERON:0004121!6.22e-22!95;UBERON:0000924!6.22e-22!95;UBERON:0006601!6.22e-22!95;UBERON:0002346!5.40e-20!64;UBERON:0003075!5.40e-20!64;UBERON:0007284!5.40e-20!64;UBERON:0000073!1.13e-18!54;UBERON:0001017!1.66e-17!73;UBERON:0001016!2.56e-17!75;UBERON:0001049!3.76e-17!52;UBERON:0005068!3.76e-17!52;UBERON:0006241!3.76e-17!52;UBERON:0007135!3.76e-17!52;UBERON:0003056!7.59e-16!49;UBERON:0000955!2.69e-14!47;UBERON:0006238!2.69e-14!47;UBERON:0002616!1.28e-13!46;UBERON:0010314!4.83e-13!92;UBERON:0003080!1.41e-12!40;UBERON:0002020!1.55e-12!34;UBERON:0002780!6.43e-12!39;UBERON:0001890!6.43e-12!39;UBERON:0006240!6.43e-12!39;UBERON:0003528!8.74e-10!29;UBERON:0002791!8.74e-10!29;UBERON:0001893!8.74e-10!29;UBERON:0000489!2.60e-07!21;UBERON:0002619!2.96e-07!17;UBERON:0002021!3.89e-07!10;UBERON:0000411!3.89e-07!10;UBERON:0001950!3.89e-07!10
|tfbs_overrepresentation_for_novel_motifs=0.438063,2.48969,0.411716,0.480627,0.299217,0.495263,0.587291,0.594722,0.616096,0.826837,0.542749,0.575086,0.206435,0.599731,1.53029,0,0.795315,0.792229,0.19222,2.3823,0.374752,0.27937,0.598814,0.29769,0.419327,0.62766,1.63893,0.516511,0.344372,0.446946,0.50223,0.897561,0.78719,0.964228,0.848378,0.101236,0.766323,0.57142,0.258564,0.230656,0.295233,0.507468,0.54842,0.851774,0.515031,0.469348,0.714592,0.532496,0.219744,0.347313,0.777641,0.654933,1.3744,1.04034,1.0579,1.47583,0.356236,1.3814,0.522357,0.604914,0.877332,0.664501,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,1.01778,0.21183,0.293368,1.09164,0.97874,2.14449,0.498755,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,0.200155,0.975495,0.339494,0.042613,0.145788,1.71058,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,0.203879,0.913319,0.71485,0.79664,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,1.10097,1.02459,0.380122,0.547992,1.27206,0.293461,2.11126,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,1.67446,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.275843,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,1.26636,0.717753,2.03691,0.448938,0.813943,0.452587,0.256263,1.04192,1.95942,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,1.09603,0.767269,0.612377,0.278874,0.573477,2.88237
|tfbs_overrepresentation_for_novel_motifs=0.438063,2.48969,0.411716,0.480627,0.299217,0.495263,0.587291,0.594722,0.616096,0.826837,0.542749,0.575086,0.206435,0.599731,1.53029,0,0.795315,0.792229,0.19222,2.3823,0.374752,0.27937,0.598814,0.29769,0.419327,0.62766,1.63893,0.516511,0.344372,0.446946,0.50223,0.897561,0.78719,0.964228,0.848378,0.101236,0.766323,0.57142,0.258564,0.230656,0.295233,0.507468,0.54842,0.851774,0.515031,0.469348,0.714592,0.532496,0.219744,0.347313,0.777641,0.654933,1.3744,1.04034,1.0579,1.47583,0.356236,1.3814,0.522357,0.604914,0.877332,0.664501,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,1.01778,0.21183,0.293368,1.09164,0.97874,2.14449,0.498755,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,0.200155,0.975495,0.339494,0.042613,0.145788,1.71058,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,0.203879,0.913319,0.71485,0.79664,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,1.10097,1.02459,0.380122,0.547992,1.27206,0.293461,2.11126,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,1.67446,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.275843,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,1.26636,0.717753,2.03691,0.448938,0.813943,0.452587,0.256263,1.04192,1.95942,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,1.09603,0.767269,0.612377,0.278874,0.573477,2.88237
|tfbs_overrepresentation_jaspar=MA0003.1;1.4232,MA0004.1;0.481116,MA0006.1;0.311391,MA0007.1;0.465969,MA0009.1;2.13157,MA0014.1;0.694761,MA0017.1;0.337808,MA0019.1;0.740036,MA0024.1;0.880057,MA0025.1;2.60917,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;0.128106,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;0.648475,MA0056.1;0,MA0057.1;0.376102,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;0.232592,MA0061.1;6.77693,MA0063.1;0,MA0066.1;1.49567,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;0.046559,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;2.67639,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;1.84519,MA0103.1;0.348572,MA0105.1;7.33458,MA0106.1;0.677988,MA0107.1;4.38636,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;0.311187,MA0117.1;0.992087,MA0119.1;1.04809,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;2.4049,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;0.631666,MA0146.1;2.04073,MA0147.1;0.274511,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.967192,MA0035.2;0.573016,MA0039.2;1.06357,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;0.365364,MA0104.2;0.218974,MA0047.2;0.626803,MA0112.2;0.0910939,MA0065.2;1.0577,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.397336,MA0155.1;0.336768,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;2.11316,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;0.246285,MA0259.1;0.26402,MA0442.1;0
}}
}}

Revision as of 12:56, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr2:58999674..58999693,+p4@Pkp4
Mm9::chr4:101180704..101180735,+p2@Dnajc6
Mm9::chr6:24903644..24903650,-p@chr6:24903644..24903650
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Mm9::chr6:24906071..24906105,-p1@Tmem229a
Mm9::chr6:24906106..24906131,-p2@Tmem229a
Mm9::chr6:24906348..24906371,-p3@Tmem229a
Mm9::chr8:93657848..93657921,-p1@Aktip


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:0032092positive regulation of protein binding0.0226799604204372
GO:0043393regulation of protein binding0.0264527057129833
GO:0051099positive regulation of binding0.0264527057129833
GO:0051098regulation of binding0.0395726164332678
GO:0033240positive regulation of amine metabolic process0.0395726164332678
GO:0045764positive regulation of amino acid metabolic process0.0395726164332678
GO:0001934positive regulation of protein amino acid phosphorylation0.0395726164332678
GO:0006793phosphorus metabolic process0.0395726164332678
GO:0006796phosphate metabolic process0.0395726164332678
GO:0031072heat shock protein binding0.0395726164332678
GO:0001932regulation of protein amino acid phosphorylation0.0395726164332678
GO:0033238regulation of amine metabolic process0.0395726164332678
GO:0006521regulation of amino acid metabolic process0.0395726164332678
GO:0042325regulation of phosphorylation0.0395726164332678
GO:0051174regulation of phosphorus metabolic process0.0395726164332678
GO:0019220regulation of phosphate metabolic process0.0395726164332678



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
ecto-epithelium3.55e-2273
ectoderm-derived structure6.22e-2295
ectoderm6.22e-2295
presumptive ectoderm6.22e-2295
neurectoderm5.40e-2064
neural plate5.40e-2064
presumptive neural plate5.40e-2064
regional part of nervous system1.13e-1854
central nervous system1.66e-1773
nervous system2.56e-1775
neural tube3.76e-1752
neural rod3.76e-1752
future spinal cord3.76e-1752
neural keel3.76e-1752
pre-chordal neural plate7.59e-1649
brain2.69e-1447
future brain2.69e-1447
regional part of brain1.28e-1346
structure with developmental contribution from neural crest4.83e-1392
anterior neural tube1.41e-1240
gray matter1.55e-1234
regional part of forebrain6.43e-1239
forebrain6.43e-1239
future forebrain6.43e-1239
brain grey matter8.74e-1029
regional part of telencephalon8.74e-1029
telencephalon8.74e-1029
cavitated compound organ2.60e-0721
regional part of cerebral cortex2.96e-0717
occipital lobe3.89e-0710
visual cortex3.89e-0710
neocortex3.89e-0710


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
MA0007.10.465969
MA0009.12.13157
MA0014.10.694761
MA0017.10.337808
MA0019.10.740036
MA0024.10.880057
MA0025.12.60917
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
MA0048.10.128106
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.648475
MA0056.10
MA0057.10.376102
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.16.77693
MA0063.10
MA0066.11.49567
MA0067.11.27078
MA0068.10.121435
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
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
MA0088.12.67639
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.11.84519
MA0103.10.348572
MA0105.17.33458
MA0106.10.677988
MA0107.14.38636
MA0108.20.763162
MA0109.10
MA0111.10.460823
MA0113.10.649407
MA0114.10.719313
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
MA0135.12.4049
MA0136.10.600242
MA0139.10.202522
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.631666
MA0146.12.04073
MA0147.10.274511
MA0148.10.49752
MA0149.10.411562
MA0062.20.967192
MA0035.20.573016
MA0039.21.06357
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.20.218974
MA0047.20.626803
MA0112.20.0910939
MA0065.21.0577
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.397336
MA0155.10.336768
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.10.302441
MA0163.12.11316
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.21.96358
MA0102.21.65195
MA0258.10.246285
MA0259.10.26402
MA0442.10
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