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MCL coexpression mm9:1006: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0010314!2.61e-26!92;UBERON:0004121!3.93e-21!95;UBERON:0000924!3.93e-21!95;UBERON:0006601!3.93e-21!95;UBERON:0000073!8.65e-21!54;UBERON:0001017!6.33e-20!73;UBERON:0002346!9.60e-20!64;UBERON:0003075!9.60e-20!64;UBERON:0007284!9.60e-20!64;UBERON:0001016!1.58e-19!75;UBERON:0010371!1.90e-19!73;UBERON:0001049!2.49e-19!52;UBERON:0005068!2.49e-19!52;UBERON:0006241!2.49e-19!52;UBERON:0007135!2.49e-19!52;UBERON:0000955!1.09e-16!47;UBERON:0006238!1.09e-16!47;UBERON:0002616!4.68e-16!46;UBERON:0002020!6.04e-15!34;UBERON:0003056!1.17e-14!49;UBERON:0003080!1.10e-13!40;UBERON:0004111!2.40e-13!122;UBERON:0000025!3.65e-13!114;UBERON:0002780!4.69e-13!39;UBERON:0001890!4.69e-13!39;UBERON:0006240!4.69e-13!39;UBERON:0003528!2.40e-12!29;UBERON:0002791!2.40e-12!29;UBERON:0001893!2.40e-12!29;UBERON:0000956!1.76e-08!21;UBERON:0001869!1.76e-08!21;UBERON:0000203!1.76e-08!21;UBERON:0002619!4.35e-08!17;UBERON:0002021!2.45e-07!10;UBERON:0000411!2.45e-07!10;UBERON:0001950!2.45e-07!10;UBERON:0000468!5.99e-07!333
|ontology_enrichment_uberon=UBERON:0010314!2.61e-26!92;UBERON:0004121!3.93e-21!95;UBERON:0000924!3.93e-21!95;UBERON:0006601!3.93e-21!95;UBERON:0000073!8.65e-21!54;UBERON:0001017!6.33e-20!73;UBERON:0002346!9.60e-20!64;UBERON:0003075!9.60e-20!64;UBERON:0007284!9.60e-20!64;UBERON:0001016!1.58e-19!75;UBERON:0010371!1.90e-19!73;UBERON:0001049!2.49e-19!52;UBERON:0005068!2.49e-19!52;UBERON:0006241!2.49e-19!52;UBERON:0007135!2.49e-19!52;UBERON:0000955!1.09e-16!47;UBERON:0006238!1.09e-16!47;UBERON:0002616!4.68e-16!46;UBERON:0002020!6.04e-15!34;UBERON:0003056!1.17e-14!49;UBERON:0003080!1.10e-13!40;UBERON:0004111!2.40e-13!122;UBERON:0000025!3.65e-13!114;UBERON:0002780!4.69e-13!39;UBERON:0001890!4.69e-13!39;UBERON:0006240!4.69e-13!39;UBERON:0003528!2.40e-12!29;UBERON:0002791!2.40e-12!29;UBERON:0001893!2.40e-12!29;UBERON:0000956!1.76e-08!21;UBERON:0001869!1.76e-08!21;UBERON:0000203!1.76e-08!21;UBERON:0002619!4.35e-08!17;UBERON:0002021!2.45e-07!10;UBERON:0000411!2.45e-07!10;UBERON:0001950!2.45e-07!10;UBERON:0000468!5.99e-07!333
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.369498,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.215218,0.826837,0.542749,0.575086,0.59526,0.599731,0.315771,0,0.795315,0.291368,1.06769,1.20169,1.73763,0.586604,1.45867,0.80655,1.07577,0.62766,0.542568,0.516511,0.344372,0.876948,0.50223,0.897561,0.289148,0.498917,0.316253,0.248902,1.40094,0.57142,0.258564,0.230656,0.295233,0.507468,0.258106,0.317766,0.277561,0.469348,0.714592,0.532496,0.219744,0.347313,0.777641,0.654933,0.139618,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,1.01778,0.21183,1.02583,1.09164,0.507615,0.159969,0.963958,0.703064,0.859987,0.98764,0.212973,0.812889,0.663039,0.200155,0.975495,0.613286,0.667407,0.877485,0.719558,1.70793,2.82299,0.980512,0.910485,0.305079,0.708155,0.237542,0.589174,0.913319,0.71485,0.127063,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,1.59063,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,1.45183,0.903645,1.19345,0.829907,1.00568,0.473246,1.16374,0.620831,1.29374,0.275843,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,1.70684,2.03691,0.448938,0.300961,2.05013,0.927167,1.04192,1.26486,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,2.14328,0.573477,1.42871
|tfbs_overrepresentation_for_novel_motifs=0.438063,0.369498,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.215218,0.826837,0.542749,0.575086,0.59526,0.599731,0.315771,0,0.795315,0.291368,1.06769,1.20169,1.73763,0.586604,1.45867,0.80655,1.07577,0.62766,0.542568,0.516511,0.344372,0.876948,0.50223,0.897561,0.289148,0.498917,0.316253,0.248902,1.40094,0.57142,0.258564,0.230656,0.295233,0.507468,0.258106,0.317766,0.277561,0.469348,0.714592,0.532496,0.219744,0.347313,0.777641,0.654933,0.139618,1.04034,1.0579,0.606984,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,1.01778,0.21183,1.02583,1.09164,0.507615,0.159969,0.963958,0.703064,0.859987,0.98764,0.212973,0.812889,0.663039,0.200155,0.975495,0.613286,0.667407,0.877485,0.719558,1.70793,2.82299,0.980512,0.910485,0.305079,0.708155,0.237542,0.589174,0.913319,0.71485,0.127063,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.380122,0.547992,1.27206,0.293461,1.59063,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,0.702145,1.32639,0.863723,1.45183,0.903645,1.19345,0.829907,1.00568,0.473246,1.16374,0.620831,1.29374,0.275843,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,1.70684,2.03691,0.448938,0.300961,2.05013,0.927167,1.04192,1.26486,0.619892,1.12411,0.655955,0.327731,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,2.14328,0.573477,1.42871
|tfbs_overrepresentation_jaspar=MA0003.1;0.54119,MA0004.1;0.481116,MA0006.1;0.837454,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;2.32876,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;0.801219,MA0050.1;1.29283,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;0.656954,MA0061.1;0.724575,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;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;0.285759,MA0089.1;0,MA0090.1;1.1347,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;0.488671,MA0106.1;0.677988,MA0107.1;0.906859,MA0108.2;0.763162,MA0109.1;0,MA0111.1;2.03054,MA0113.1;0.649407,MA0114.1;0.719313,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;1.05551,MA0146.1;2.04073,MA0147.1;0.753844,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.500692,MA0035.2;0.573016,MA0039.2;1.72008,MA0138.2;0.727395,MA0002.2;0.205289,MA0137.2;0.365364,MA0104.2;0.624968,MA0047.2;0.626803,MA0112.2;0.304722,MA0065.2;0.305574,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;1.07519,MA0154.1;0.126143,MA0155.1;1.13804,MA0156.1;0.356017,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.284457,MA0160.1;0.50056,MA0161.1;0,MA0162.1;0.878466,MA0163.1;0.0280055,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;0.610433,MA0099.2;0.721008,MA0079.2;0.105858,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;1.34223,MA0442.1;0
}}
}}

Revision as of 12:39, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:11063185..11063304,+p1@Epm2a
Mm9::chr16:7341612..7341617,+p@chr16:7341612..7341617
+
Mm9::chr2:119420024..119420068,+p1@1700020I14Rik
Mm9::chr2:180891698..180891722,-p2@Eef1a2
Mm9::chr2:180891726..180891747,-p3@Eef1a2
Mm9::chr2:31951038..31951115,+p1@Ppapdc3
Mm9::chr8:124102655..124102717,-p1@Fbxo31


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:0051440regulation of ubiquitin-protein ligase activity during meiotic cell cycle0.00497765533650046
GO:0051352negative regulation of ligase activity0.00497765533650046
GO:0051444negative regulation of ubiquitin-protein ligase activity0.00497765533650046
GO:0007056spindle assembly involved in female meiosis0.00497765533650046
GO:0051442negative regulation of ubiquitin-protein ligase activity during meiotic cell cycle0.00497765533650046
GO:0007057spindle assembly involved in female meiosis I0.00497765533650046
GO:0051438regulation of ubiquitin-protein ligase activity0.00497765533650046
GO:0051340regulation of ligase activity0.00871018095320527
GO:0007144female meiosis I0.0104513581438009
GO:0046785microtubule polymerization0.0104513581438009
GO:0000089mitotic metaphase0.0116116657850133
GO:0040020regulation of meiosis0.0116116657850133
GO:0005853eukaryotic translation elongation factor 1 complex0.0124400480142583
GO:0001556oocyte maturation0.0124400480142583
GO:0051225spindle assembly0.0130609769002419
GO:0051323metaphase0.0130609769002419
GO:0009994oocyte differentiation0.0146625460840285
GO:0007143female meiosis0.0146625460840285
GO:0048599oocyte development0.0146625460840285
GO:0007128meiotic prophase I0.0149231506590364
GO:0051324prophase0.0149231506590364
GO:0016050vesicle organization and biogenesis0.0189884181220496
GO:0031109microtubule polymerization or depolymerization0.0203037202757398
GO:0007051spindle organization and biogenesis0.0203037202757398
GO:0007346regulation of progression through mitotic cell cycle0.0278313726471385
GO:0048477oogenesis0.0280966723473018
GO:0016787hydrolase activity0.0297494731467228
GO:0007281germ cell development0.0335274459548965
GO:0007127meiosis I0.0335675056197165
GO:0006073glucan metabolic process0.0336715916646123
GO:0005977glycogen metabolic process0.0336715916646123
GO:0003746translation elongation factor activity0.0336715916646123
GO:0006112energy reserve metabolic process0.0357361588570191
GO:0008138protein tyrosine/serine/threonine phosphatase activity0.0357361588570191
GO:0007292female gamete generation0.0357361588570191
GO:0051258protein polymerization0.0376294963705317
GO:0006414translational elongation0.0401854718817365
GO:0005976polysaccharide metabolic process0.0401854718817365
GO:0044264cellular polysaccharide metabolic process0.0401854718817365
GO:0043086negative regulation of catalytic activity0.0401854718817365
GO:0044267cellular protein metabolic process0.0401854718817365
GO:0044260cellular macromolecule metabolic process0.0410341441179329
GO:0019538protein metabolic process0.0431625958879685
GO:0032502developmental process0.0463267450141775
GO:0000226microtubule cytoskeleton organization and biogenesis0.04866852896075
GO:0043284biopolymer biosynthetic process0.04866852896075
GO:0015980energy derivation by oxidation of organic compounds0.04866852896075



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)2.33e-0923
neuroblast (sensu Vertebrata)2.33e-0923

Uber Anatomy
Ontology termp-valuen
structure with developmental contribution from neural crest2.61e-2692
ectoderm-derived structure3.93e-2195
ectoderm3.93e-2195
presumptive ectoderm3.93e-2195
regional part of nervous system8.65e-2154
central nervous system6.33e-2073
neurectoderm9.60e-2064
neural plate9.60e-2064
presumptive neural plate9.60e-2064
nervous system1.58e-1975
ecto-epithelium1.90e-1973
neural tube2.49e-1952
neural rod2.49e-1952
future spinal cord2.49e-1952
neural keel2.49e-1952
brain1.09e-1647
future brain1.09e-1647
regional part of brain4.68e-1646
gray matter6.04e-1534
pre-chordal neural plate1.17e-1449
anterior neural tube1.10e-1340
anatomical conduit2.40e-13122
tube3.65e-13114
regional part of forebrain4.69e-1339
forebrain4.69e-1339
future forebrain4.69e-1339
brain grey matter2.40e-1229
regional part of telencephalon2.40e-1229
telencephalon2.40e-1229
cerebral cortex1.76e-0821
cerebral hemisphere1.76e-0821
pallium1.76e-0821
regional part of cerebral cortex4.35e-0817
occipital lobe2.45e-0710
visual cortex2.45e-0710
neocortex2.45e-0710
multi-cellular organism5.99e-07333


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)
MA0003.10.54119
MA0004.10.481116
MA0006.10.837454
MA0007.10.465969
MA0009.10.92425
MA0014.12.32876
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
MA0048.10.801219
MA0050.11.29283
MA0051.10.636645
MA0052.10.945011
MA0055.10.362005
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
MA0073.10.046559
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
MA0090.11.1347
MA0091.10.494398
MA0092.10.446857
MA0093.10.329976
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.488671
MA0106.10.677988
MA0107.10.906859
MA0108.20.763162
MA0109.10
MA0111.12.03054
MA0113.10.649407
MA0114.10.719313
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
MA0145.11.05551
MA0146.12.04073
MA0147.10.753844
MA0148.10.49752
MA0149.10.411562
MA0062.20.500692
MA0035.20.573016
MA0039.21.72008
MA0138.20.727395
MA0002.20.205289
MA0137.20.365364
MA0104.20.624968
MA0047.20.626803
MA0112.20.304722
MA0065.20.305574
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.11.07519
MA0154.10.126143
MA0155.11.13804
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.284457
MA0160.10.50056
MA0161.10
MA0162.10.878466
MA0163.10.0280055
MA0164.10.600609
MA0080.20.343316
MA0018.20.610433
MA0099.20.721008
MA0079.20.105858
MA0102.21.65195
MA0258.10.246285
MA0259.11.34223
MA0442.10
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