MCL coexpression mm9:884: Difference between revisions
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{{MCL_coexpression_mm9| | 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of protein kinase B;0.00542376595628116;108686!GO:0043422;protein kinase B binding;0.00542376595628116;108686!GO:0006259;DNA metabolic process;0.029822540857081;75339,108686!GO:0006275;regulation of DNA replication;0.029822540857081;108686!GO:0051052;regulation of DNA metabolic process;0.0356792078839629;108686!GO:0032147;activation of protein kinase activity;0.0356792078839629;108686!GO:0008017;microtubule binding;0.0356792078839629;108686!GO:0006261;DNA-dependent DNA replication;0.0356792078839629;108686!GO:0019901;protein kinase binding;0.0356792078839629;108686!GO:0019900;kinase binding;0.0356792078839629;108686!GO:0001932;regulation of protein amino acid phosphorylation;0.0356792078839629;108686!GO:0033238;regulation of amine metabolic process;0.0356792078839629;108686!GO:0006521;regulation of amino acid metabolic process;0.0356792078839629;108686!GO:0015631;tubulin binding;0.0356792078839629;108686!GO:0042325;regulation of phosphorylation;0.0356792078839629;108686!GO:0051174;regulation of phosphorus metabolic process;0.0356792078839629;108686!GO:0019220;regulation of phosphate metabolic process;0.0356792078839629;108686!GO:0045860;positive regulation of protein kinase activity;0.0470658445862631;108686!GO:0033674;positive regulation of kinase activity;0.0470658445862631;108686!GO:0051347;positive regulation of transferase activity;0.0470658445862631;108686!GO:0003682;chromatin binding;0.0470658445862631;75339!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0470658445862631;75339,108686!GO:0031323;regulation of cellular metabolic process;0.0470658445862631;75339,108686!GO:0045859;regulation of protein kinase activity;0.0470658445862631;108686!GO:0019222;regulation of metabolic process;0.0470658445862631;75339,108686!GO:0006333;chromatin assembly or disassembly;0.0470658445862631;75339!GO:0043549;regulation of kinase activity;0.0470658445862631;108686!GO:0019899;enzyme binding;0.0470658445862631;108686!GO:0043085;positive regulation of catalytic activity;0.0470658445862631;108686!GO:0006260;DNA replication;0.0470658445862631;108686!GO:0051338;regulation of transferase activity;0.0470658445862631;108686!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0010314!6.05e-09!92;UBERON:0000922!5.23e-08!320;UBERON:0002021!7.68e-08!10;UBERON:0000411!7.68e-08!10;UBERON:0001950!7.68e-08!10|tfbs_overrepresentation_for_novel_motifs=0.393008,0.534222,0.367606,0.434198,0.260188,1.13872,0.538088,0.173246,0.535519,0.0447303,0.494602,0.526159,0.515774,0.550255,0.275867,0,0.742571,0.703873,0.160384,0.29826,1.58838,0.0622758,0.549359,0.717658,0.374936,0.577606,0.153291,0.469052,0.303071,0.376624,0.455168,0.843667,1.29258,0.839887,0.276324,0.60397,1.26012,0.522578,0.221921,0.195877,0.256422,0.460258,0.204736,0.27776,0.0824666,0.423266,0.662995,0.484612,0.0447507,0.305876,0.725127,0.604356,0.112729,0.985264,1.00271,0.557354,0.844204,0.513517,0.447041,0.555328,0.823643,0.613749,0.192045,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.527912,0.0665967,1.03623,0.140213,0.409836,0.136938,0.651651,0.806481,0.336166,0.179489,0.759925,1.48701,0.968721,0.920903,0.025519,0.0299392,0.118251,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.585369,0.1711,0.859272,0.663249,0.101559,0.679141,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.903338,0.333829,0.386136,0.96962,0.337254,0.499714,1.21576,0.708441,0.143112,0.437894,0.743872,0.670977,1.04163,0.692953,1.41785,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.268537,0.950857,0.427043,1.10792,0.570914,1.23736,0.061199,0.401212,1.16726,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,1.04134,0.724779,0.120154,0.0553085,0.986833,0.207643,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,0.240994,0.524587,0.166768|tfbs_overrepresentation_jaspar=MA0003.1;0.0545917,MA0004.1;0.434673,MA0006.1;0.271714,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;0.012738,MA0017.1;0.296816,MA0019.1;0.688051,MA0024.1;0.826339,MA0025.1;1.10341,MA0027.1;2.51754,MA0028.1;0.281528,MA0029.1;0.804619,MA0030.1;0.811181,MA0031.1;0.775627,MA0038.1;0.577528,MA0040.1;0.882616,MA0041.1;0.360875,MA0042.1;0.348174,MA0043.1;0.966833,MA0046.1;0.906029,MA0048.1;1.13456,MA0050.1;0.472794,MA0051.1;0.586414,MA0052.1;0.890676,MA0055.1;0.523649,MA0056.1;0,MA0057.1;0.0935008,MA0058.1;0.341628,MA0059.1;0.353484,MA0060.1;0.197678,MA0061.1;0.638933,MA0063.1;0,MA0066.1;0.566617,MA0067.1;1.21448,MA0068.1;0.0965831,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;1.1212e-05,MA0074.1;0.531046,MA0076.1;0.315013,MA0077.1;0.851175,MA0078.1;0.61926,MA0081.1;0.375851,MA0083.1;0.96604,MA0084.1;1.54225,MA0087.1;0.922929,MA0088.1;0.229377,MA0089.1;0,MA0090.1;0.401197,MA0091.1;0.447561,MA0092.1;0.401504,MA0093.1;0.289361,MA0095.1;0,MA0098.1;0,MA0100.1;0.519598,MA0101.1;0.362124,MA0103.1;0.307078,MA0105.1;0.133231,MA0106.1;0.626997,MA0107.1;0.301222,MA0108.2;0.710846,MA0109.1;0,MA0111.1;0.415012,MA0113.1;0.598933,MA0114.1;0.222763,MA0115.1;0.969632,MA0116.1;0.27152,MA0117.1;0.937363,MA0119.1;0.362692,MA0122.1;0.957212,MA0124.1;1.16127,MA0125.1;1.0872,MA0130.1;0,MA0131.1;0.683521,MA0132.1;0,MA0133.1;0,MA0135.1;1.00325,MA0136.1;0.550755,MA0139.1;0.169849,MA0140.1;0.519484,MA0141.1;0.325895,MA0142.1;0.761136,MA0143.1;1.49307,MA0144.1;0.225588,MA0145.1;0.527241,MA0146.1;0.198184,MA0147.1;0.236889,MA0148.1;0.450593,MA0149.1;0.367458,MA0062.2;0.137653,MA0035.2;0.524137,MA0039.2;0.00106576,MA0138.2;0.675599,MA0002.2;0.172399,MA0137.2;0.32312,MA0104.2;0.18504,MA0047.2;0.576767,MA0112.2;0.0701537,MA0065.2;0.0704227,MA0150.1;0.419883,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.100744,MA0155.1;0.0804339,MA0156.1;0.314185,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.246253,MA0160.1;0.453546,MA0161.1;0,MA0162.1;0.0211019,MA0163.1;0.0836563,MA0164.1;0.551114,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;1.25307e-05,MA0102.2;1.59466,MA0258.1;0.210437,MA0259.1;0.227035,MA0442.1;0}} | ||
Latest revision as of 16:02, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr11:102342088..102342102,- | p@chr11:102342088..102342102 - |
| Mm9::chr11:29363676..29363691,+ | p4@Ccdc88a |
| Mm9::chr11:29363735..29363749,+ | p3@Ccdc88a |
| Mm9::chr11:77107497..77107501,+ | p@chr11:77107497..77107501 + |
| Mm9::chr14:57291296..57291310,+ | p2@Mphosph8 |
| Mm9::chr14:57292752..57292765,+ | p@chr14:57292752..57292765 + |
| Mm9::chr14:57293460..57293463,+ | p@chr14:57293460..57293463 + |
| Mm9::chr19:60018977..60019003,- | p4@Rab11fip2 |
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:0032148 | activation of protein kinase B | 0.00542376595628116 |
| GO:0043422 | protein kinase B binding | 0.00542376595628116 |
| GO:0006259 | DNA metabolic process | 0.029822540857081 |
| GO:0006275 | regulation of DNA replication | 0.029822540857081 |
| GO:0051052 | regulation of DNA metabolic process | 0.0356792078839629 |
| GO:0032147 | activation of protein kinase activity | 0.0356792078839629 |
| GO:0008017 | microtubule binding | 0.0356792078839629 |
| GO:0006261 | DNA-dependent DNA replication | 0.0356792078839629 |
| GO:0019901 | protein kinase binding | 0.0356792078839629 |
| GO:0019900 | kinase binding | 0.0356792078839629 |
| GO:0001932 | regulation of protein amino acid phosphorylation | 0.0356792078839629 |
| GO:0033238 | regulation of amine metabolic process | 0.0356792078839629 |
| GO:0006521 | regulation of amino acid metabolic process | 0.0356792078839629 |
| GO:0015631 | tubulin binding | 0.0356792078839629 |
| GO:0042325 | regulation of phosphorylation | 0.0356792078839629 |
| GO:0051174 | regulation of phosphorus metabolic process | 0.0356792078839629 |
| GO:0019220 | regulation of phosphate metabolic process | 0.0356792078839629 |
| GO:0045860 | positive regulation of protein kinase activity | 0.0470658445862631 |
| GO:0033674 | positive regulation of kinase activity | 0.0470658445862631 |
| GO:0051347 | positive regulation of transferase activity | 0.0470658445862631 |
| GO:0003682 | chromatin binding | 0.0470658445862631 |
| GO:0019219 | regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0470658445862631 |
| GO:0031323 | regulation of cellular metabolic process | 0.0470658445862631 |
| GO:0045859 | regulation of protein kinase activity | 0.0470658445862631 |
| GO:0019222 | regulation of metabolic process | 0.0470658445862631 |
| GO:0006333 | chromatin assembly or disassembly | 0.0470658445862631 |
| GO:0043549 | regulation of kinase activity | 0.0470658445862631 |
| GO:0019899 | enzyme binding | 0.0470658445862631 |
| GO:0043085 | positive regulation of catalytic activity | 0.0470658445862631 |
| GO:0006260 | DNA replication | 0.0470658445862631 |
| GO:0051338 | regulation of transferase activity | 0.0470658445862631 |
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>
| Ontology term | p-value | n |
|---|---|---|
| structure with developmental contribution from neural crest | 6.05e-09 | 92 |
| embryo | 5.23e-08 | 320 |
| occipital lobe | 7.68e-08 | 10 |
| visual cortex | 7.68e-08 | 10 |
| neocortex | 7.68e-08 | 10 |
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 | 0.0545917 |
| MA0004.1 | 0.434673 |
| MA0006.1 | 0.271714 |
| MA0007.1 | 0.419994 |
| MA0009.1 | 0.870101 |
| MA0014.1 | 0.012738 |
| MA0017.1 | 0.296816 |
| MA0019.1 | 0.688051 |
| MA0024.1 | 0.826339 |
| MA0025.1 | 1.10341 |
| MA0027.1 | 2.51754 |
| MA0028.1 | 0.281528 |
| MA0029.1 | 0.804619 |
| MA0030.1 | 0.811181 |
| MA0031.1 | 0.775627 |
| MA0038.1 | 0.577528 |
| MA0040.1 | 0.882616 |
| MA0041.1 | 0.360875 |
| MA0042.1 | 0.348174 |
| MA0043.1 | 0.966833 |
| MA0046.1 | 0.906029 |
| MA0048.1 | 1.13456 |
| MA0050.1 | 0.472794 |
| MA0051.1 | 0.586414 |
| MA0052.1 | 0.890676 |
| MA0055.1 | 0.523649 |
| MA0056.1 | 0 |
| MA0057.1 | 0.0935008 |
| MA0058.1 | 0.341628 |
| MA0059.1 | 0.353484 |
| MA0060.1 | 0.197678 |
| MA0061.1 | 0.638933 |
| MA0063.1 | 0 |
| MA0066.1 | 0.566617 |
| MA0067.1 | 1.21448 |
| MA0068.1 | 0.0965831 |
| MA0069.1 | 0.891016 |
| MA0070.1 | 0.881319 |
| MA0071.1 | 0.471969 |
| MA0072.1 | 0.872842 |
| MA0073.1 | 1.1212e-05 |
| MA0074.1 | 0.531046 |
| MA0076.1 | 0.315013 |
| MA0077.1 | 0.851175 |
| MA0078.1 | 0.61926 |
| MA0081.1 | 0.375851 |
| MA0083.1 | 0.96604 |
| MA0084.1 | 1.54225 |
| MA0087.1 | 0.922929 |
| MA0088.1 | 0.229377 |
| MA0089.1 | 0 |
| MA0090.1 | 0.401197 |
| MA0091.1 | 0.447561 |
| MA0092.1 | 0.401504 |
| MA0093.1 | 0.289361 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.519598 |
| MA0101.1 | 0.362124 |
| MA0103.1 | 0.307078 |
| MA0105.1 | 0.133231 |
| MA0106.1 | 0.626997 |
| MA0107.1 | 0.301222 |
| MA0108.2 | 0.710846 |
| MA0109.1 | 0 |
| MA0111.1 | 0.415012 |
| MA0113.1 | 0.598933 |
| MA0114.1 | 0.222763 |
| MA0115.1 | 0.969632 |
| MA0116.1 | 0.27152 |
| MA0117.1 | 0.937363 |
| MA0119.1 | 0.362692 |
| MA0122.1 | 0.957212 |
| MA0124.1 | 1.16127 |
| MA0125.1 | 1.0872 |
| MA0130.1 | 0 |
| MA0131.1 | 0.683521 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.00325 |
| MA0136.1 | 0.550755 |
| MA0139.1 | 0.169849 |
| MA0140.1 | 0.519484 |
| MA0141.1 | 0.325895 |
| MA0142.1 | 0.761136 |
| MA0143.1 | 1.49307 |
| MA0144.1 | 0.225588 |
| MA0145.1 | 0.527241 |
| MA0146.1 | 0.198184 |
| MA0147.1 | 0.236889 |
| MA0148.1 | 0.450593 |
| MA0149.1 | 0.367458 |
| MA0062.2 | 0.137653 |
| MA0035.2 | 0.524137 |
| MA0039.2 | 0.00106576 |
| MA0138.2 | 0.675599 |
| MA0002.2 | 0.172399 |
| MA0137.2 | 0.32312 |
| MA0104.2 | 0.18504 |
| MA0047.2 | 0.576767 |
| MA0112.2 | 0.0701537 |
| MA0065.2 | 0.0704227 |
| MA0150.1 | 0.419883 |
| MA0151.1 | 0 |
| MA0152.1 | 0.576873 |
| MA0153.1 | 1.01988 |
| MA0154.1 | 0.100744 |
| MA0155.1 | 0.0804339 |
| MA0156.1 | 0.314185 |
| MA0157.1 | 0.729116 |
| MA0158.1 | 0 |
| MA0159.1 | 0.246253 |
| MA0160.1 | 0.453546 |
| MA0161.1 | 0 |
| MA0162.1 | 0.0211019 |
| MA0163.1 | 0.0836563 |
| MA0164.1 | 0.551114 |
| MA0080.2 | 0.302064 |
| MA0018.2 | 0.560731 |
| MA0099.2 | 0.669311 |
| MA0079.2 | 1.25307e-05 |
| MA0102.2 | 1.59466 |
| MA0258.1 | 0.210437 |
| MA0259.1 | 0.227035 |
| MA0442.1 | 0 |
