MCL coexpression mm9:1006: Difference between revisions
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{{MCL_coexpression_mm9| | 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of ubiquitin-protein ligase activity during meiotic cell cycle;0.00497765533650046;67141!GO:0051352;negative regulation of ligase activity;0.00497765533650046;67141!GO:0051444;negative regulation of ubiquitin-protein ligase activity;0.00497765533650046;67141!GO:0007056;spindle assembly involved in female meiosis;0.00497765533650046;67141!GO:0051442;negative regulation of ubiquitin-protein ligase activity during meiotic cell cycle;0.00497765533650046;67141!GO:0007057;spindle assembly involved in female meiosis I;0.00497765533650046;67141!GO:0051438;regulation of ubiquitin-protein ligase activity;0.00497765533650046;67141!GO:0051340;regulation of ligase activity;0.00871018095320527;67141!GO:0007144;female meiosis I;0.0104513581438009;67141!GO:0046785;microtubule polymerization;0.0104513581438009;67141!GO:0000089;mitotic metaphase;0.0116116657850133;67141!GO:0040020;regulation of meiosis;0.0116116657850133;67141!GO:0005853;eukaryotic translation elongation factor 1 complex;0.0124400480142583;13628!GO:0001556;oocyte maturation;0.0124400480142583;67141!GO:0051225;spindle assembly;0.0130609769002419;67141!GO:0051323;metaphase;0.0130609769002419;67141!GO:0009994;oocyte differentiation;0.0146625460840285;67141!GO:0007143;female meiosis;0.0146625460840285;67141!GO:0048599;oocyte development;0.0146625460840285;67141!GO:0007128;meiotic prophase I;0.0149231506590364;67141!GO:0051324;prophase;0.0149231506590364;67141!GO:0016050;vesicle organization and biogenesis;0.0189884181220496;67141!GO:0031109;microtubule polymerization or depolymerization;0.0203037202757398;67141!GO:0007051;spindle organization and biogenesis;0.0203037202757398;67141!GO:0007346;regulation of progression through mitotic cell cycle;0.0278313726471385;67141!GO:0048477;oogenesis;0.0280966723473018;67141!GO:0016787;hydrolase activity;0.0297494731467228;13628,227721,13853!GO:0007281;germ cell development;0.0335274459548965;67141!GO:0007127;meiosis I;0.0335675056197165;67141!GO:0006073;glucan metabolic process;0.0336715916646123;13853!GO:0005977;glycogen metabolic process;0.0336715916646123;13853!GO:0003746;translation elongation factor activity;0.0336715916646123;13628!GO:0006112;energy reserve metabolic process;0.0357361588570191;13853!GO:0008138;protein tyrosine/serine/threonine phosphatase activity;0.0357361588570191;13853!GO:0007292;female gamete generation;0.0357361588570191;67141!GO:0051258;protein polymerization;0.0376294963705317;67141!GO:0006414;translational elongation;0.0401854718817365;13628!GO:0005976;polysaccharide metabolic process;0.0401854718817365;13853!GO:0044264;cellular polysaccharide metabolic process;0.0401854718817365;13853!GO:0043086;negative regulation of catalytic activity;0.0401854718817365;67141!GO:0044267;cellular protein metabolic process;0.0401854718817365;13628,67141,13853!GO:0044260;cellular macromolecule metabolic process;0.0410341441179329;13628,67141,13853!GO:0019538;protein metabolic process;0.0431625958879685;13628,67141,13853!GO:0032502;developmental process;0.0463267450141775;13628,67141,13853!GO:0000226;microtubule cytoskeleton organization and biogenesis;0.04866852896075;67141!GO:0043284;biopolymer biosynthetic process;0.04866852896075;13628!GO:0015980;energy derivation by oxidation of organic compounds;0.04866852896075;13853!|ontology_enrichment_celltype=CL:0000117!2.33e-09!23;CL:0000337!2.33e-09!23|ontology_enrichment_disease=|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_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}} | ||
Latest revision as of 16:14, 17 September 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 ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0051440 | regulation of ubiquitin-protein ligase activity during meiotic cell cycle | 0.00497765533650046 |
| GO:0051352 | negative regulation of ligase activity | 0.00497765533650046 |
| GO:0051444 | negative regulation of ubiquitin-protein ligase activity | 0.00497765533650046 |
| GO:0007056 | spindle assembly involved in female meiosis | 0.00497765533650046 |
| GO:0051442 | negative regulation of ubiquitin-protein ligase activity during meiotic cell cycle | 0.00497765533650046 |
| GO:0007057 | spindle assembly involved in female meiosis I | 0.00497765533650046 |
| GO:0051438 | regulation of ubiquitin-protein ligase activity | 0.00497765533650046 |
| GO:0051340 | regulation of ligase activity | 0.00871018095320527 |
| GO:0007144 | female meiosis I | 0.0104513581438009 |
| GO:0046785 | microtubule polymerization | 0.0104513581438009 |
| GO:0000089 | mitotic metaphase | 0.0116116657850133 |
| GO:0040020 | regulation of meiosis | 0.0116116657850133 |
| GO:0005853 | eukaryotic translation elongation factor 1 complex | 0.0124400480142583 |
| GO:0001556 | oocyte maturation | 0.0124400480142583 |
| GO:0051225 | spindle assembly | 0.0130609769002419 |
| GO:0051323 | metaphase | 0.0130609769002419 |
| GO:0009994 | oocyte differentiation | 0.0146625460840285 |
| GO:0007143 | female meiosis | 0.0146625460840285 |
| GO:0048599 | oocyte development | 0.0146625460840285 |
| GO:0007128 | meiotic prophase I | 0.0149231506590364 |
| GO:0051324 | prophase | 0.0149231506590364 |
| GO:0016050 | vesicle organization and biogenesis | 0.0189884181220496 |
| GO:0031109 | microtubule polymerization or depolymerization | 0.0203037202757398 |
| GO:0007051 | spindle organization and biogenesis | 0.0203037202757398 |
| GO:0007346 | regulation of progression through mitotic cell cycle | 0.0278313726471385 |
| GO:0048477 | oogenesis | 0.0280966723473018 |
| GO:0016787 | hydrolase activity | 0.0297494731467228 |
| GO:0007281 | germ cell development | 0.0335274459548965 |
| GO:0007127 | meiosis I | 0.0335675056197165 |
| GO:0006073 | glucan metabolic process | 0.0336715916646123 |
| GO:0005977 | glycogen metabolic process | 0.0336715916646123 |
| GO:0003746 | translation elongation factor activity | 0.0336715916646123 |
| GO:0006112 | energy reserve metabolic process | 0.0357361588570191 |
| GO:0008138 | protein tyrosine/serine/threonine phosphatase activity | 0.0357361588570191 |
| GO:0007292 | female gamete generation | 0.0357361588570191 |
| GO:0051258 | protein polymerization | 0.0376294963705317 |
| GO:0006414 | translational elongation | 0.0401854718817365 |
| GO:0005976 | polysaccharide metabolic process | 0.0401854718817365 |
| GO:0044264 | cellular polysaccharide metabolic process | 0.0401854718817365 |
| GO:0043086 | negative regulation of catalytic activity | 0.0401854718817365 |
| GO:0044267 | cellular protein metabolic process | 0.0401854718817365 |
| GO:0044260 | cellular macromolecule metabolic process | 0.0410341441179329 |
| GO:0019538 | protein metabolic process | 0.0431625958879685 |
| GO:0032502 | developmental process | 0.0463267450141775 |
| GO:0000226 | microtubule cytoskeleton organization and biogenesis | 0.04866852896075 |
| GO:0043284 | biopolymer biosynthetic process | 0.04866852896075 |
| GO:0015980 | energy derivation by oxidation of organic compounds | 0.04866852896075 |
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>
| Ontology term | p-value | n |
|---|---|---|
| CNS neuron (sensu Vertebrata) | 2.33e-09 | 23 |
| neuroblast (sensu Vertebrata) | 2.33e-09 | 23 |
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) |
|---|---|
| MA0003.1 | 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 |
