MCL coexpression mm9:841: Difference between revisions
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{{MCL_coexpression_mm9| | 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dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity;0.00928461847680428;109264!GO:0004738;pyruvate dehydrogenase activity;0.00928461847680428;18597!GO:0008090;retrograde axon cargo transport;0.00928461847680428;13518!GO:0004739;pyruvate dehydrogenase (acetyl-transferring) activity;0.00928461847680428;18597!GO:0044262;cellular carbohydrate metabolic process;0.00928461847680428;109264,18597!GO:0031122;cytoplasmic microtubule organization and biogenesis;0.00928461847680428;13518!GO:0004470;malic enzyme activity;0.00928461847680428;109264!GO:0006108;malate metabolic process;0.0103156775094049;109264!GO:0005975;carbohydrate metabolic process;0.0104423344548168;109264,18597!GO:0016624;oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor;0.0104423344548168;18597!GO:0016615;malate dehydrogenase activity;0.0104423344548168;109264!GO:0009925;basal plasma membrane;0.0104423344548168;13518!GO:0060053;neurofilament cytoskeleton;0.0104423344548168;13518!GO:0045178;basal part of cell;0.0104423344548168;13518!GO:0043648;dicarboxylic acid metabolic process;0.0104423344548168;109264!GO:0008088;axon cargo transport;0.0109194899359178;13518!GO:0031110;regulation of microtubule polymerization or depolymerization;0.0134045032055733;13518!GO:0031109;microtubule polymerization or depolymerization;0.0136750999806115;13518!GO:0006100;tricarboxylic acid cycle intermediate metabolic process;0.0139185353958062;109264!GO:0051287;NAD binding;0.019434306341141;109264!GO:0044444;cytoplasmic part;0.0241329633513848;109264,18597,13518!GO:0016491;oxidoreductase activity;0.0246206447328127;109264,18597!GO:0030055;cell-matrix junction;0.0270341658124554;13518!GO:0016903;oxidoreductase activity, acting on the aldehyde or oxo group of donors;0.0281726907363467;18597!GO:0005739;mitochondrion;0.0293869201483859;109264,18597!GO:0006096;glycolysis;0.0293869201483859;18597!GO:0007050;cell cycle arrest;0.0293869201483859;13518!GO:0008017;microtubule binding;0.0293869201483859;13518!GO:0006007;glucose catabolic process;0.0296262072510759;18597!GO:0046365;monosaccharide catabolic process;0.0296262072510759;18597!GO:0019320;hexose catabolic process;0.0296262072510759;18597!GO:0051128;regulation of cellular component organization and biogenesis;0.0296262072510759;13518!GO:0015631;tubulin binding;0.0296262072510759;13518!GO:0046164;alcohol catabolic process;0.0296262072510759;18597!GO:0000226;microtubule cytoskeleton organization and biogenesis;0.0329035671846674;13518!GO:0044275;cellular carbohydrate catabolic process;0.0330111061329209;18597!GO:0016323;basolateral plasma membrane;0.0340829371096963;13518!GO:0016052;carbohydrate catabolic process;0.0341540971008432;18597!GO:0007018;microtubule-based movement;0.0383646209931261;13518!GO:0006006;glucose metabolic process;0.0431054408632943;18597!GO:0030705;cytoskeleton-dependent intracellular transport;0.0431054408632943;13518!GO:0016616;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;0.0472273373491732;109264!GO:0050662;coenzyme binding;0.0475000923347259;109264!GO:0045786;negative regulation of progression through cell cycle;0.0475000923347259;13518!GO:0016614;oxidoreductase activity, acting on CH-OH group of donors;0.0475000923347259;109264!GO:0045111;intermediate filament cytoskeleton;0.0475000923347259;13518!GO:0019318;hexose metabolic process;0.0499452758871698;18597!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0004535!6.86e-08!23;UBERON:0001009!6.86e-08!23;UBERON:0007100!4.71e-07!18;UBERON:0000948!4.71e-07!18;UBERON:0005498!4.71e-07!18;UBERON:0004140!4.71e-07!18;UBERON:0009881!4.71e-07!18;UBERON:0004141!4.71e-07!18;UBERON:0003084!4.71e-07!18;UBERON:0007005!4.71e-07!18;UBERON:0004139!4.71e-07!18;UBERON:0004291!4.71e-07!18|tfbs_overrepresentation_for_novel_motifs=0.354643,0.706384,0.330161,1.02163,0.645379,1.05171,0.495658,0.146465,0.468136,0.0330111,0.453212,0.484001,0.88117,0.507558,1.9552,0,0.696644,0.22065,0.134657,0.528436,0.296085,0.179861,0.50668,0.226287,1.60644,0.534339,0.801525,0.428336,1.35822,0.319094,0.414842,0.796599,0.218674,0.113369,0.242923,0.281474,0.604998,0.480503,1.67947,0.167387,0.224094,0.419787,0.0422275,0.244285,0.317317,0.998423,0.618203,0.443479,0.314152,0.745859,0.679429,0.560572,0.30602,0.937018,0.954342,0.514504,0.279148,1.18878,0.12126,0.512521,0.776777,0.569793,0.163832,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.31262,0.151245,0.424998,0.987652,0.748687,0.107966,0.735293,0.607043,2.99702,0.299972,0.152219,0.713779,0.568383,0.14134,0.873141,0.395495,0.439624,0.319367,0.623015,1.60001,1.15927,0.878077,0.809272,0.657661,0.188213,0.17334,0.444003,1.90157,0.618454,0.278788,0.605162,0.796322,0.919715,0.680015,0.678976,1.07585,0.737915,0.439611,0.821842,0.297733,0.348012,0.921485,0.301014,0.458194,1.16629,0.222515,1.15833,0.398075,0.697928,0.207304,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.235546,0.90286,1.00644,1.05894,0.527782,1.18781,0.0467191,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,1.50578,1.92834,0.364791,0.229209,1.10522,0.659481,0.938577,1.01208,0.526881,1.01974,0.561556,0.253271,0.352329,0.362302,1.1483,3.34905,0.763895,0.345891,2.71035,0.519673,0.602679,0.482466,0.0435162|tfbs_overrepresentation_jaspar=MA0003.1;0.662116,MA0004.1;0.394951,MA0006.1;0.670874,MA0007.1;0.38073,MA0009.1;0.82278,MA0014.1;0.248772,MA0017.1;0.26239,MA0019.1;0.642876,MA0024.1;0.779446,MA0025.1;1.05446,MA0027.1;2.46647,MA0028.1;0.24786,MA0029.1;0.757957,MA0030.1;0.764448,MA0031.1;0.729293,MA0038.1;0.534262,MA0040.1;0.835181,MA0041.1;0.323687,MA0042.1;0.311486,MA0043.1;0.918718,MA0046.1;0.858391,MA0048.1;0.0824771,MA0050.1;1.10321,MA0051.1;1.34084,MA0052.1;0.84317,MA0055.1;1.02213,MA0056.1;0,MA0057.1;0.549903,MA0058.1;0.305206,MA0059.1;0.849123,MA0060.1;0.169058,MA0061.1;0.194456,MA0063.1;0,MA0066.1;0.523573,MA0067.1;1.16502,MA0068.1;0.077274,MA0069.1;0.843506,MA0070.1;3.22936,MA0071.1;1.93072,MA0072.1;0.825495,MA0073.1;0.00108891,MA0074.1;0.488775,MA0076.1;0.279739,MA0077.1;0.804033,MA0078.1;0.575205,MA0081.1;0.338098,MA0083.1;0.917931,MA0084.1;1.49188,MA0087.1;0.87515,MA0088.1;0.18495,MA0089.1;0,MA0090.1;0.362551,MA0091.1;0.407455,MA0092.1;0.362847,MA0093.1;0.2553,MA0095.1;0,MA0098.1;0,MA0100.1;0.477594,MA0101.1;0.324888,MA0103.1;0.748482,MA0105.1;0.35523,MA0106.1;0.582805,MA0107.1;0.266586,MA0108.2;0.665343,MA0109.1;0,MA0111.1;0.375908,MA0113.1;1.36684,MA0114.1;0.19245,MA0115.1;0.921497,MA0116.1;0.238371,MA0117.1;0.88947,MA0119.1;1.56471,MA0122.1;0.909168,MA0124.1;1.11203,MA0125.1;1.03833,MA0130.1;0,MA0131.1;0.638414,MA0132.1;0,MA0133.1;0,MA0135.1;0.954884,MA0136.1;0.508047,MA0139.1;0.143341,MA0140.1;0.477483,MA0141.1;3.05378,MA0142.1;0.714976,MA0143.1;0.571221,MA0144.1;0.195095,MA0145.1;0.0543321,MA0146.1;0.0111657,MA0147.1;0.593505,MA0148.1;2.78137,MA0149.1;0.330018,MA0062.2;0.365726,MA0035.2;0.482026,MA0039.2;0.0946163,MA0138.2;2.58639,MA0002.2;0.877049,MA0137.2;0.287486,MA0104.2;0.926067,MA0047.2;2.27139,MA0112.2;0.442124,MA0065.2;0.44341,MA0150.1;0.380623,MA0151.1;0,MA0152.1;0.53362,MA0153.1;0.971406,MA0154.1;0.0809407,MA0155.1;0.0631765,MA0156.1;0.278949,MA0157.1;0.683365,MA0158.1;0,MA0159.1;1.15501,MA0160.1;2.79475,MA0161.1;0,MA0162.1;0.0143037,MA0163.1;0.321031,MA0164.1;0.508398,MA0080.2;0.267388,MA0018.2;0.51781,MA0099.2;0.624421,MA0079.2;0.0880689,MA0102.2;1.5442,MA0258.1;0.180934,MA0259.1;0.196451,MA0442.1;0}} | ||
Latest revision as of 15:58, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr1:34178286..34178303,+ | p11@Dst |
| Mm9::chr1:34178314..34178329,+ | p7@Dst |
| Mm9::chr5:122068874..122068934,- | p1@Acad12 |
| Mm9::chr6:86466214..86466234,- | p1@uc009csb.1 |
| Mm9::chr6:86466248..86466270,- | p3@uc009csb.1 |
| Mm9::chr6:86466277..86466290,- | p4@uc009csb.1 |
| Mm9::chr7:96781385..96781422,+ | p2@Me3 |
| Mm9::chr7:96781461..96781503,+ | p5@Me3 |
| Mm9::chrX:156576281..156576303,- | p1@Pdha1 |
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:0030056 | hemidesmosome | 0.00928461847680428 |
| GO:0004473 | malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity | 0.00928461847680428 |
| GO:0004738 | pyruvate dehydrogenase activity | 0.00928461847680428 |
| GO:0008090 | retrograde axon cargo transport | 0.00928461847680428 |
| GO:0004739 | pyruvate dehydrogenase (acetyl-transferring) activity | 0.00928461847680428 |
| GO:0044262 | cellular carbohydrate metabolic process | 0.00928461847680428 |
| GO:0031122 | cytoplasmic microtubule organization and biogenesis | 0.00928461847680428 |
| GO:0004470 | malic enzyme activity | 0.00928461847680428 |
| GO:0006108 | malate metabolic process | 0.0103156775094049 |
| GO:0005975 | carbohydrate metabolic process | 0.0104423344548168 |
| GO:0016624 | oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor | 0.0104423344548168 |
| GO:0016615 | malate dehydrogenase activity | 0.0104423344548168 |
| GO:0009925 | basal plasma membrane | 0.0104423344548168 |
| GO:0060053 | neurofilament cytoskeleton | 0.0104423344548168 |
| GO:0045178 | basal part of cell | 0.0104423344548168 |
| GO:0043648 | dicarboxylic acid metabolic process | 0.0104423344548168 |
| GO:0008088 | axon cargo transport | 0.0109194899359178 |
| GO:0031110 | regulation of microtubule polymerization or depolymerization | 0.0134045032055733 |
| GO:0031109 | microtubule polymerization or depolymerization | 0.0136750999806115 |
| GO:0006100 | tricarboxylic acid cycle intermediate metabolic process | 0.0139185353958062 |
| GO:0051287 | NAD binding | 0.019434306341141 |
| GO:0044444 | cytoplasmic part | 0.0241329633513848 |
| GO:0016491 | oxidoreductase activity | 0.0246206447328127 |
| GO:0030055 | cell-matrix junction | 0.0270341658124554 |
| GO:0016903 | oxidoreductase activity, acting on the aldehyde or oxo group of donors | 0.0281726907363467 |
| GO:0005739 | mitochondrion | 0.0293869201483859 |
| GO:0006096 | glycolysis | 0.0293869201483859 |
| GO:0007050 | cell cycle arrest | 0.0293869201483859 |
| GO:0008017 | microtubule binding | 0.0293869201483859 |
| GO:0006007 | glucose catabolic process | 0.0296262072510759 |
| GO:0046365 | monosaccharide catabolic process | 0.0296262072510759 |
| GO:0019320 | hexose catabolic process | 0.0296262072510759 |
| GO:0051128 | regulation of cellular component organization and biogenesis | 0.0296262072510759 |
| GO:0015631 | tubulin binding | 0.0296262072510759 |
| GO:0046164 | alcohol catabolic process | 0.0296262072510759 |
| GO:0000226 | microtubule cytoskeleton organization and biogenesis | 0.0329035671846674 |
| GO:0044275 | cellular carbohydrate catabolic process | 0.0330111061329209 |
| GO:0016323 | basolateral plasma membrane | 0.0340829371096963 |
| GO:0016052 | carbohydrate catabolic process | 0.0341540971008432 |
| GO:0007018 | microtubule-based movement | 0.0383646209931261 |
| GO:0006006 | glucose metabolic process | 0.0431054408632943 |
| GO:0030705 | cytoskeleton-dependent intracellular transport | 0.0431054408632943 |
| GO:0016616 | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | 0.0472273373491732 |
| GO:0050662 | coenzyme binding | 0.0475000923347259 |
| GO:0045786 | negative regulation of progression through cell cycle | 0.0475000923347259 |
| GO:0016614 | oxidoreductase activity, acting on CH-OH group of donors | 0.0475000923347259 |
| GO:0045111 | intermediate filament cytoskeleton | 0.0475000923347259 |
| GO:0019318 | hexose metabolic process | 0.0499452758871698 |
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 |
|---|---|---|
| cardiovascular system | 6.86e-08 | 23 |
| circulatory system | 6.86e-08 | 23 |
| primary circulatory organ | 4.71e-07 | 18 |
| heart | 4.71e-07 | 18 |
| primitive heart tube | 4.71e-07 | 18 |
| primary heart field | 4.71e-07 | 18 |
| anterior lateral plate mesoderm | 4.71e-07 | 18 |
| heart tube | 4.71e-07 | 18 |
| heart primordium | 4.71e-07 | 18 |
| cardiac mesoderm | 4.71e-07 | 18 |
| cardiogenic plate | 4.71e-07 | 18 |
| heart rudiment | 4.71e-07 | 18 |
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 | 0.662116 |
| MA0004.1 | 0.394951 |
| MA0006.1 | 0.670874 |
| MA0007.1 | 0.38073 |
| MA0009.1 | 0.82278 |
| MA0014.1 | 0.248772 |
| MA0017.1 | 0.26239 |
| MA0019.1 | 0.642876 |
| MA0024.1 | 0.779446 |
| MA0025.1 | 1.05446 |
| MA0027.1 | 2.46647 |
| MA0028.1 | 0.24786 |
| MA0029.1 | 0.757957 |
| MA0030.1 | 0.764448 |
| MA0031.1 | 0.729293 |
| MA0038.1 | 0.534262 |
| MA0040.1 | 0.835181 |
| MA0041.1 | 0.323687 |
| MA0042.1 | 0.311486 |
| MA0043.1 | 0.918718 |
| MA0046.1 | 0.858391 |
| MA0048.1 | 0.0824771 |
| MA0050.1 | 1.10321 |
| MA0051.1 | 1.34084 |
| MA0052.1 | 0.84317 |
| MA0055.1 | 1.02213 |
| MA0056.1 | 0 |
| MA0057.1 | 0.549903 |
| MA0058.1 | 0.305206 |
| MA0059.1 | 0.849123 |
| MA0060.1 | 0.169058 |
| MA0061.1 | 0.194456 |
| MA0063.1 | 0 |
| MA0066.1 | 0.523573 |
| MA0067.1 | 1.16502 |
| MA0068.1 | 0.077274 |
| MA0069.1 | 0.843506 |
| MA0070.1 | 3.22936 |
| MA0071.1 | 1.93072 |
| MA0072.1 | 0.825495 |
| MA0073.1 | 0.00108891 |
| MA0074.1 | 0.488775 |
| MA0076.1 | 0.279739 |
| MA0077.1 | 0.804033 |
| MA0078.1 | 0.575205 |
| MA0081.1 | 0.338098 |
| MA0083.1 | 0.917931 |
| MA0084.1 | 1.49188 |
| MA0087.1 | 0.87515 |
| MA0088.1 | 0.18495 |
| MA0089.1 | 0 |
| MA0090.1 | 0.362551 |
| MA0091.1 | 0.407455 |
| MA0092.1 | 0.362847 |
| MA0093.1 | 0.2553 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.477594 |
| MA0101.1 | 0.324888 |
| MA0103.1 | 0.748482 |
| MA0105.1 | 0.35523 |
| MA0106.1 | 0.582805 |
| MA0107.1 | 0.266586 |
| MA0108.2 | 0.665343 |
| MA0109.1 | 0 |
| MA0111.1 | 0.375908 |
| MA0113.1 | 1.36684 |
| MA0114.1 | 0.19245 |
| MA0115.1 | 0.921497 |
| MA0116.1 | 0.238371 |
| MA0117.1 | 0.88947 |
| MA0119.1 | 1.56471 |
| MA0122.1 | 0.909168 |
| MA0124.1 | 1.11203 |
| MA0125.1 | 1.03833 |
| MA0130.1 | 0 |
| MA0131.1 | 0.638414 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.954884 |
| MA0136.1 | 0.508047 |
| MA0139.1 | 0.143341 |
| MA0140.1 | 0.477483 |
| MA0141.1 | 3.05378 |
| MA0142.1 | 0.714976 |
| MA0143.1 | 0.571221 |
| MA0144.1 | 0.195095 |
| MA0145.1 | 0.0543321 |
| MA0146.1 | 0.0111657 |
| MA0147.1 | 0.593505 |
| MA0148.1 | 2.78137 |
| MA0149.1 | 0.330018 |
| MA0062.2 | 0.365726 |
| MA0035.2 | 0.482026 |
| MA0039.2 | 0.0946163 |
| MA0138.2 | 2.58639 |
| MA0002.2 | 0.877049 |
| MA0137.2 | 0.287486 |
| MA0104.2 | 0.926067 |
| MA0047.2 | 2.27139 |
| MA0112.2 | 0.442124 |
| MA0065.2 | 0.44341 |
| MA0150.1 | 0.380623 |
| MA0151.1 | 0 |
| MA0152.1 | 0.53362 |
| MA0153.1 | 0.971406 |
| MA0154.1 | 0.0809407 |
| MA0155.1 | 0.0631765 |
| MA0156.1 | 0.278949 |
| MA0157.1 | 0.683365 |
| MA0158.1 | 0 |
| MA0159.1 | 1.15501 |
| MA0160.1 | 2.79475 |
| MA0161.1 | 0 |
| MA0162.1 | 0.0143037 |
| MA0163.1 | 0.321031 |
| MA0164.1 | 0.508398 |
| MA0080.2 | 0.267388 |
| MA0018.2 | 0.51781 |
| MA0099.2 | 0.624421 |
| MA0079.2 | 0.0880689 |
| MA0102.2 | 1.5442 |
| MA0258.1 | 0.180934 |
| MA0259.1 | 0.196451 |
| MA0442.1 | 0 |
