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MCL coexpression mm9:1049: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001017!2.62e-29!73;UBERON:0001016!6.27e-28!75;UBERON:0004121!3.13e-27!95;UBERON:0000924!3.13e-27!95;UBERON:0006601!3.13e-27!95;UBERON:0002346!2.23e-25!64;UBERON:0003075!2.23e-25!64;UBERON:0007284!2.23e-25!64;UBERON:0010371!7.33e-20!73;UBERON:0003056!1.43e-18!49;UBERON:0001049!3.67e-17!52;UBERON:0005068!3.67e-17!52;UBERON:0006241!3.67e-17!52;UBERON:0007135!3.67e-17!52;UBERON:0000073!4.53e-17!54;UBERON:0010314!1.16e-14!92;UBERON:0000955!2.23e-14!47;UBERON:0006238!2.23e-14!47;UBERON:0002616!6.86e-14!46;UBERON:0003080!2.02e-13!40;UBERON:0002780!7.63e-13!39;UBERON:0001890!7.63e-13!39;UBERON:0006240!7.63e-13!39;UBERON:0002410!7.94e-10!9;UBERON:0002020!1.30e-09!34;UBERON:0001894!1.13e-07!10;UBERON:0006222!1.13e-07!10;UBERON:0000010!2.01e-07!11;UBERON:0000007!2.95e-07!8;UBERON:0003296!2.95e-07!8;UBERON:0010133!2.95e-07!8;UBERON:0003528!3.41e-07!29;UBERON:0002791!3.41e-07!29;UBERON:0001893!3.41e-07!29
|ontology_enrichment_uberon=UBERON:0001017!2.62e-29!73;UBERON:0001016!6.27e-28!75;UBERON:0004121!3.13e-27!95;UBERON:0000924!3.13e-27!95;UBERON:0006601!3.13e-27!95;UBERON:0002346!2.23e-25!64;UBERON:0003075!2.23e-25!64;UBERON:0007284!2.23e-25!64;UBERON:0010371!7.33e-20!73;UBERON:0003056!1.43e-18!49;UBERON:0001049!3.67e-17!52;UBERON:0005068!3.67e-17!52;UBERON:0006241!3.67e-17!52;UBERON:0007135!3.67e-17!52;UBERON:0000073!4.53e-17!54;UBERON:0010314!1.16e-14!92;UBERON:0000955!2.23e-14!47;UBERON:0006238!2.23e-14!47;UBERON:0002616!6.86e-14!46;UBERON:0003080!2.02e-13!40;UBERON:0002780!7.63e-13!39;UBERON:0001890!7.63e-13!39;UBERON:0006240!7.63e-13!39;UBERON:0002410!7.94e-10!9;UBERON:0002020!1.30e-09!34;UBERON:0001894!1.13e-07!10;UBERON:0006222!1.13e-07!10;UBERON:0000010!2.01e-07!11;UBERON:0000007!2.95e-07!8;UBERON:0003296!2.95e-07!8;UBERON:0010133!2.95e-07!8;UBERON:0003528!3.41e-07!29;UBERON:0002791!3.41e-07!29;UBERON:0001893!3.41e-07!29
|tfbs_overrepresentation_for_novel_motifs=1.11639,0.161863,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.616096,0.478312,0.542749,0.575086,0.206435,0.599731,0.315771,0,0.795315,0.291368,1.06769,0.731589,0.374752,0.27937,0.598814,0.29769,0.419327,0.62766,0.542568,0.516511,0.344372,0.446946,0.50223,0.897561,0.78719,0.498917,0.848378,0.248902,0.279977,1.40099,1.32199,0.230656,0.295233,0.507468,0.258106,0.317766,0.515031,0.469348,0.714592,0.532496,0.219744,0.917701,0.777641,0.654933,0.431711,1.04034,1.0579,1.47583,0.356236,0.56214,0.522357,0.604914,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.608073,0.293368,1.09164,0.97874,0.482617,0.498755,0.703064,0.859987,0.378988,0.610783,0.812889,0.663039,0.580284,0.975495,0.339494,1.0354,0.447265,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.668513,0.589174,0.913319,0.71485,0.127063,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,1.12953,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,1.45183,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,0.446555,1.26843,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,1.13988,0.300961,0.147909,0.256263,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,0.435579,1.13413,1.25393,0.974632,0.864173,0.428662,1.80928,0.612377,0.763807,0.573477,0.433127
|tfbs_overrepresentation_for_novel_motifs=1.11639,0.161863,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.616096,0.478312,0.542749,0.575086,0.206435,0.599731,0.315771,0,0.795315,0.291368,1.06769,0.731589,0.374752,0.27937,0.598814,0.29769,0.419327,0.62766,0.542568,0.516511,0.344372,0.446946,0.50223,0.897561,0.78719,0.498917,0.848378,0.248902,0.279977,1.40099,1.32199,0.230656,0.295233,0.507468,0.258106,0.317766,0.515031,0.469348,0.714592,0.532496,0.219744,0.917701,0.777641,0.654933,0.431711,1.04034,1.0579,1.47583,0.356236,0.56214,0.522357,0.604914,0.877332,0.664501,0.642748,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.608073,0.293368,1.09164,0.97874,0.482617,0.498755,0.703064,0.859987,0.378988,0.610783,0.812889,0.663039,0.580284,0.975495,0.339494,1.0354,0.447265,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.668513,0.589174,0.913319,0.71485,0.127063,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,1.12953,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,1.45183,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,0.446555,1.26843,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,1.13988,0.300961,0.147909,0.256263,1.04192,0.243291,0.619892,1.12411,0.655955,0.327731,0.435579,1.13413,1.25393,0.974632,0.864173,0.428662,1.80928,0.612377,0.763807,0.573477,0.433127
|tfbs_overrepresentation_jaspar=MA0003.1;0.0861444,MA0004.1;0.481116,MA0006.1;0.311391,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;1.30252,MA0050.1;0.520357,MA0051.1;1.53797,MA0052.1;0.945011,MA0055.1;3.04444,MA0056.1;0,MA0057.1;0.756125,MA0058.1;0.384683,MA0059.1;0.397033,MA0060.1;0.232592,MA0061.1;0.261749,MA0063.1;0,MA0066.1;1.49567,MA0067.1;1.27078,MA0068.1;0.385183,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;0.519509,MA0072.1;0.927016,MA0073.1;0.152496,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;0.0841779,MA0089.1;0,MA0090.1;1.1347,MA0091.1;1.23749,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;0.162418,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;0.259463,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;0.568252,MA0141.1;0.368264,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.262477,MA0145.1;0.304732,MA0146.1;0.108739,MA0147.1;0.274511,MA0148.1;1.24416,MA0149.1;0.411562,MA0062.2;0.167299,MA0035.2;0.573016,MA0039.2;0.219063,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;0.365364,MA0104.2;0.624968,MA0047.2;0.626803,MA0112.2;0.0910939,MA0065.2;0.0914071,MA0150.1;1.17631,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;1.4173,MA0160.1;0.50056,MA0161.1;0,MA0162.1;0.127623,MA0163.1;0.519779,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;0.705112,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;0.729797,MA0442.1;0
}}
}}

Revision as of 12:44, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:86954204..86954231,-p@chr10:86954204..86954231
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Mm9::chr10:86954608..86954619,-p@chr10:86954608..86954619
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Mm9::chr10:86955227..86955238,-p@chr10:86955227..86955238
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Mm9::chr10:86956396..86956411,-p1@Ascl1
Mm9::chr13:83871972..83871975,+p2@C130071C03Rik
Mm9::chr5:124801192..124801233,-p4@Cdk2ap1
Mm9::chr7:29086791..29086810,-p1@Dll3


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:0001709cell fate determination0.000516535071736775
GO:0007219Notch signaling pathway0.00114520659288295
GO:0045165cell fate commitment0.00213663507368652
GO:0014017neuroblast fate commitment0.00213663507368652
GO:0014016neuroblast differentiation0.00213663507368652
GO:0007400neuroblast fate determination0.00213663507368652
GO:0060165regulation of timing of subpallium neuron differentiation0.00213663507368652
GO:0060164regulation of timing of neuron differentiation0.00213663507368652
GO:0060163subpallium neuron fate commitment0.00379825424110381
GO:0007389pattern specification process0.00506273949032288
GO:0048505regulation of timing of cell differentiation0.00610333384880086
GO:0007386compartment specification0.00610333384880086
GO:0040034regulation of development, heterochronic0.00610333384880086
GO:0021544subpallium development0.00610333384880086
GO:0005112Notch binding0.00683535936358031
GO:0048339paraxial mesoderm development0.0138789988942662
GO:0007399nervous system development0.0199200831650066
GO:0048663neuron fate commitment0.0199200831650066
GO:0021537telencephalon development0.0206666928430308
GO:0007405neuroblast proliferation0.0219455261865678
GO:0045664regulation of neuron differentiation0.0219455261865678
GO:0001756somitogenesis0.0255946941180428
GO:0010001glial cell differentiation0.0281835305557912
GO:0042063gliogenesis0.0286519160840723
GO:0035282segmentation0.0286519160840723
GO:0007498mesoderm development0.0321292377309846
GO:0001764neuron migration0.0347163224574104



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>

Uber Anatomy
Ontology termp-valuen
central nervous system2.62e-2973
nervous system6.27e-2875
ectoderm-derived structure3.13e-2795
ectoderm3.13e-2795
presumptive ectoderm3.13e-2795
neurectoderm2.23e-2564
neural plate2.23e-2564
presumptive neural plate2.23e-2564
ecto-epithelium7.33e-2073
pre-chordal neural plate1.43e-1849
neural tube3.67e-1752
neural rod3.67e-1752
future spinal cord3.67e-1752
neural keel3.67e-1752
regional part of nervous system4.53e-1754
structure with developmental contribution from neural crest1.16e-1492
brain2.23e-1447
future brain2.23e-1447
regional part of brain6.86e-1446
anterior neural tube2.02e-1340
regional part of forebrain7.63e-1339
forebrain7.63e-1339
future forebrain7.63e-1339
autonomic nervous system7.94e-109
gray matter1.30e-0934
diencephalon1.13e-0710
future diencephalon1.13e-0710
peripheral nervous system2.01e-0711
pituitary gland2.95e-078
gland of diencephalon2.95e-078
neuroendocrine gland2.95e-078
brain grey matter3.41e-0729
regional part of telencephalon3.41e-0729
telencephalon3.41e-0729


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)
MA0003.10.0861444
MA0004.10.481116
MA0006.10.311391
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
MA0048.11.30252
MA0050.10.520357
MA0051.11.53797
MA0052.10.945011
MA0055.13.04444
MA0056.10
MA0057.10.756125
MA0058.10.384683
MA0059.10.397033
MA0060.10.232592
MA0061.10.261749
MA0063.10
MA0066.11.49567
MA0067.11.27078
MA0068.10.385183
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.10.152496
MA0074.10.580087
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.0841779
MA0089.10
MA0090.11.1347
MA0091.11.23749
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.162418
MA0106.10.677988
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
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.304732
MA0146.10.108739
MA0147.10.274511
MA0148.11.24416
MA0149.10.411562
MA0062.20.167299
MA0035.20.573016
MA0039.20.219063
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.20.624968
MA0047.20.626803
MA0112.20.0910939
MA0065.20.0914071
MA0150.11.17631
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.397336
MA0155.10.336768
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.11.4173
MA0160.10.50056
MA0161.10
MA0162.10.127623
MA0163.10.519779
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.20.705112
MA0102.21.65195
MA0258.10.246285
MA0259.10.729797
MA0442.10
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