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MCL coexpression mm9:1187: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002346!5.60e-17!64;UBERON:0003075!5.60e-17!64;UBERON:0007284!5.60e-17!64;UBERON:0004121!3.72e-16!95;UBERON:0000924!3.72e-16!95;UBERON:0006601!3.72e-16!95;UBERON:0001017!3.85e-16!73;UBERON:0010371!6.57e-16!73;UBERON:0010314!2.21e-15!92;UBERON:0001016!5.22e-15!75;UBERON:0000073!7.66e-15!54;UBERON:0001049!5.01e-14!52;UBERON:0005068!5.01e-14!52;UBERON:0006241!5.01e-14!52;UBERON:0007135!5.01e-14!52;UBERON:0000468!4.38e-12!333;UBERON:0003056!2.06e-11!49;UBERON:0000955!1.16e-10!47;UBERON:0006238!1.16e-10!47;UBERON:0002616!1.47e-10!46;UBERON:0000922!2.00e-09!320;UBERON:0003080!1.95e-08!40;UBERON:0002780!6.19e-08!39;UBERON:0001890!6.19e-08!39;UBERON:0006240!6.19e-08!39;UBERON:0003076!3.03e-07!12;UBERON:0003057!3.03e-07!12;UBERON:0002020!4.74e-07!34;UBERON:0000479!5.68e-07!349
|ontology_enrichment_uberon=UBERON:0002346!5.60e-17!64;UBERON:0003075!5.60e-17!64;UBERON:0007284!5.60e-17!64;UBERON:0004121!3.72e-16!95;UBERON:0000924!3.72e-16!95;UBERON:0006601!3.72e-16!95;UBERON:0001017!3.85e-16!73;UBERON:0010371!6.57e-16!73;UBERON:0010314!2.21e-15!92;UBERON:0001016!5.22e-15!75;UBERON:0000073!7.66e-15!54;UBERON:0001049!5.01e-14!52;UBERON:0005068!5.01e-14!52;UBERON:0006241!5.01e-14!52;UBERON:0007135!5.01e-14!52;UBERON:0000468!4.38e-12!333;UBERON:0003056!2.06e-11!49;UBERON:0000955!1.16e-10!47;UBERON:0006238!1.16e-10!47;UBERON:0002616!1.47e-10!46;UBERON:0000922!2.00e-09!320;UBERON:0003080!1.95e-08!40;UBERON:0002780!6.19e-08!39;UBERON:0001890!6.19e-08!39;UBERON:0006240!6.19e-08!39;UBERON:0003076!3.03e-07!12;UBERON:0003057!3.03e-07!12;UBERON:0002020!4.74e-07!34;UBERON:0000479!5.68e-07!349
|tfbs_overrepresentation_for_novel_motifs=0.438063,1.45672,0.411716,0.480627,0.299217,0.495263,1.43443,0.206208,0.215218,3.57215,0.542749,0.575086,0.206435,0.599731,0.315771,0,0.795315,0.291368,1.06769,0.361892,0.374752,0.27937,0.598814,0.29769,2.82296,0.62766,0.184473,0.516511,0.344372,0.876948,0.50223,0.897561,0.289148,0.166577,0.316253,3.01978,0.279977,0.57142,0.258564,0.652422,0.800988,0.507468,0.258106,0.317766,2.10004,1.18381,0.714592,0.532496,0.0609361,1.64197,1.83068,0.654933,0.139618,1.04034,1.0579,0.606984,2.52498,2.36496,0.176152,0.604914,3.36473,2.69491,1.20126,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,1.79967,0.21183,1.02583,1.09164,2.96143,0.159969,0.166511,0.703064,0.859987,1.75229,0.212973,0.812889,0.663039,1.09903,0.975495,2.36627,0.042613,2.03326,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,0.203879,0.913319,0.71485,0.127063,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,1.74385,1.10097,1.02459,0.380122,0.547992,1.27206,0.796976,1.12953,2.10934,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,2.62204,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.452587,0.927167,1.04192,0.243291,1.5029,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,2.52772,2.14328,0.573477,1.42871
|tfbs_overrepresentation_for_novel_motifs=0.438063,1.45672,0.411716,0.480627,0.299217,0.495263,1.43443,0.206208,0.215218,3.57215,0.542749,0.575086,0.206435,0.599731,0.315771,0,0.795315,0.291368,1.06769,0.361892,0.374752,0.27937,0.598814,0.29769,2.82296,0.62766,0.184473,0.516511,0.344372,0.876948,0.50223,0.897561,0.289148,0.166577,0.316253,3.01978,0.279977,0.57142,0.258564,0.652422,0.800988,0.507468,0.258106,0.317766,2.10004,1.18381,0.714592,0.532496,0.0609361,1.64197,1.83068,0.654933,0.139618,1.04034,1.0579,0.606984,2.52498,2.36496,0.176152,0.604914,3.36473,2.69491,1.20126,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,1.79967,0.21183,1.02583,1.09164,2.96143,0.159969,0.166511,0.703064,0.859987,1.75229,0.212973,0.812889,0.663039,1.09903,0.975495,2.36627,0.042613,2.03326,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,0.203879,0.913319,0.71485,0.127063,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,1.74385,1.10097,1.02459,0.380122,0.547992,1.27206,0.796976,1.12953,2.10934,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,2.62204,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.452587,0.927167,1.04192,0.243291,1.5029,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,2.52772,2.14328,0.573477,1.42871
|tfbs_overrepresentation_jaspar=MA0003.1;1.8002,MA0004.1;0.481116,MA0006.1;1.51462,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;0.222567,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;0.62758,MA0040.1;0.936879,MA0041.1;0.404721,MA0042.1;0.391504,MA0043.1;1.02178,MA0046.1;0.960497,MA0048.1;0.40238,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;0.157978,MA0056.1;0,MA0057.1;1.23731,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;0.232592,MA0061.1;1.33382,MA0063.1;0,MA0066.1;0.616444,MA0067.1;1.27078,MA0068.1;8.4178,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;0.519509,MA0072.1;0.927016,MA0073.1;1.06143,MA0074.1;0.580087,MA0076.1;0.938908,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;1.00582,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;0.348572,MA0105.1;2.88877,MA0106.1;1.62423,MA0107.1;0.342432,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;2.38485,MA0141.1;0.368264,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.262477,MA0145.1;0.304732,MA0146.1;2.04073,MA0147.1;2.12106,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.500692,MA0035.2;2.40034,MA0039.2;0.113749,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;0.365364,MA0104.2;1.82979,MA0047.2;0.626803,MA0112.2;0.631649,MA0065.2;0.0914071,MA0150.1;1.17631,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;1.29007,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;0.55478,MA0163.1;0.82914,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;0.559163,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;0.729797,MA0442.1;0
}}
}}

Revision as of 12:56, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr2:28302351..28302398,+p1@Ppp1r26
Mm9::chr8:90483459..90483475,-p1@Zfp423
Mm9::chr8:90484484..90484518,-p@chr8:90484484..90484518
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Mm9::chr8:90484519..90484541,-p@chr8:90484519..90484541
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Mm9::chr8:90484545..90484560,-p@chr8:90484545..90484560
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Mm9::chr8:90484561..90484593,-p@chr8:90484561..90484593
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Mm9::chr8:90484611..90484622,-p@chr8:90484611..90484622
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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

no results for this coexpression

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)6.68e-1423
neuroblast (sensu Vertebrata)6.68e-1423
neuron5.51e-1033
neuronal stem cell5.51e-1033
neuroblast5.51e-1033
electrically signaling cell5.51e-1033
ectodermal cell8.27e-1044
neurectodermal cell8.27e-1044
neural cell1.54e-0943

Uber Anatomy
Ontology termp-valuen
neurectoderm5.60e-1764
neural plate5.60e-1764
presumptive neural plate5.60e-1764
ectoderm-derived structure3.72e-1695
ectoderm3.72e-1695
presumptive ectoderm3.72e-1695
central nervous system3.85e-1673
ecto-epithelium6.57e-1673
structure with developmental contribution from neural crest2.21e-1592
nervous system5.22e-1575
regional part of nervous system7.66e-1554
neural tube5.01e-1452
neural rod5.01e-1452
future spinal cord5.01e-1452
neural keel5.01e-1452
multi-cellular organism4.38e-12333
pre-chordal neural plate2.06e-1149
brain1.16e-1047
future brain1.16e-1047
regional part of brain1.47e-1046
embryo2.00e-09320
anterior neural tube1.95e-0840
regional part of forebrain6.19e-0839
forebrain6.19e-0839
future forebrain6.19e-0839
posterior neural tube3.03e-0712
chordal neural plate3.03e-0712
gray matter4.74e-0734
tissue5.68e-07349


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)
MA0003.11.8002
MA0004.10.481116
MA0006.11.51462
MA0007.10.465969
MA0009.10.92425
MA0014.10.222567
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
MA0048.10.40238
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.157978
MA0056.10
MA0057.11.23731
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.11.33382
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.18.4178
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.11.06143
MA0074.10.580087
MA0076.10.938908
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
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.12.88877
MA0106.11.62423
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
MA0119.10.40661
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
MA0140.12.38485
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.304732
MA0146.12.04073
MA0147.12.12106
MA0148.10.49752
MA0149.10.411562
MA0062.20.500692
MA0035.22.40034
MA0039.20.113749
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.21.82979
MA0047.20.626803
MA0112.20.631649
MA0065.20.0914071
MA0150.11.17631
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.11.29007
MA0155.10.336768
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.10.55478
MA0163.10.82914
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.20.559163
MA0102.21.65195
MA0258.10.246285
MA0259.10.729797
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:1187&oldid=2574582"