MCL coexpression mm9:635: Difference between revisions
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{{MCL_coexpression_mm9 | 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catabolic process;0.000719686101583094;17448,18293!GO:0046365;monosaccharide catabolic process;0.000719686101583094;17448,18293!GO:0019320;hexose catabolic process;0.000719686101583094;17448,18293!GO:0046164;alcohol catabolic process;0.000719686101583094;17448,18293!GO:0044275;cellular carbohydrate catabolic process;0.000835044202329801;17448,18293!GO:0016052;carbohydrate catabolic process;0.000852708932219754;17448,18293!GO:0006006;glucose metabolic process;0.00135788563649404;17448,18293!GO:0005739;mitochondrion;0.0017805292280721;17448,18747,18293!GO:0019318;hexose metabolic process;0.0017805292280721;17448,18293!GO:0005996;monosaccharide metabolic process;0.0017805292280721;17448,18293!GO:0050164;oxoglutarate dehydrogenase (NADP+) activity;0.0017805292280721;18293!GO:0004591;oxoglutarate dehydrogenase (succinyl-transferring) activity;0.00305216858660128;18293!GO:0004691;cAMP-dependent protein kinase activity;0.00305216858660128;18747!GO:0044265;cellular macromolecule catabolic process;0.00377011932676117;17448,18293!GO:0030976;thiamin pyrophosphate binding;0.00377011932676117;18293!GO:0030060;L-malate dehydrogenase activity;0.00377011932676117;17448!GO:0044262;cellular carbohydrate metabolic process;0.0039228738921035;17448,18293!GO:0006066;alcohol metabolic process;0.0039228738921035;17448,18293!GO:0004690;cyclic nucleotide-dependent protein kinase activity;0.0042725677946356;18747!GO:0009057;macromolecule catabolic process;0.00468653004588212;17448,18293!GO:0006108;malate metabolic process;0.00485492465245523;17448!GO:0005975;carbohydrate metabolic process;0.00603378529492736;17448,18293!GO:0016624;oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor;0.00622980388168085;18293!GO:0016615;malate dehydrogenase activity;0.00683461031047704;17448!GO:0044248;cellular catabolic process;0.00711899562963582;17448,18293!GO:0043648;dicarboxylic acid metabolic process;0.00711899562963582;17448!GO:0031594;neuromuscular junction;0.00991357063876156;18747!GO:0009056;catabolic process;0.0106749828994384;17448,18293!GO:0006100;tricarboxylic acid cycle intermediate metabolic process;0.0106749828994384;17448!GO:0051969;regulation of transmission of nerve impulse;0.0133400725415185;18747!GO:0050804;regulation of synaptic transmission;0.0133400725415185;18747!GO:0006099;tricarboxylic acid cycle;0.0145990669148224;17448!GO:0046356;acetyl-CoA catabolic process;0.0145990669148224;17448!GO:0001707;mesoderm formation;0.0145990669148224;18747!GO:0048332;mesoderm morphogenesis;0.0145990669148224;18747!GO:0031644;regulation of neurological process;0.0145990669148224;18747!GO:0009060;aerobic respiration;0.0145990669148224;17448!GO:0001704;formation of primary germ layer;0.0147303354289522;18747!GO:0044444;cytoplasmic part;0.0147303354289522;17448,18747,18293!GO:0009109;coenzyme catabolic process;0.0147303354289522;17448!GO:0016620;oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor;0.0147303354289522;18293!GO:0045333;cellular respiration;0.0148060594833286;17448!GO:0016491;oxidoreductase activity;0.0148060594833286;17448,18293!GO:0051187;cofactor catabolic process;0.0151680576498623;17448!GO:0006084;acetyl-CoA metabolic process;0.0157639835889618;17448!GO:0016903;oxidoreductase activity, acting on the aldehyde or oxo group of donors;0.0172399256059361;18293!GO:0007498;mesoderm development;0.0217541713803542;18747!GO:0007369;gastrulation;0.0269447198396174;18747!GO:0015980;energy derivation by oxidation of organic compounds;0.0281032602653716;17448!GO:0048729;tissue morphogenesis;0.0312938817120633;18747!GO:0019842;vitamin binding;0.0428982228502034;18293!GO:0016616;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;0.0440809510405541;17448!GO:0050662;coenzyme binding;0.0456094997535444;18293!GO:0016614;oxidoreductase activity, acting on CH-OH group of donors;0.0459307794156284;17448!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0000160!3.00e-11!31;UBERON:0000344!2.83e-08!15;UBERON:0001242!3.86e-07!13;UBERON:0000060!3.86e-07!13;UBERON:0001262!3.86e-07!13;UBERON:0004786!3.86e-07!13;UBERON:0007100!7.28e-07!18;UBERON:0000948!7.28e-07!18;UBERON:0005498!7.28e-07!18;UBERON:0004140!7.28e-07!18;UBERON:0009881!7.28e-07!18;UBERON:0004141!7.28e-07!18;UBERON:0003084!7.28e-07!18;UBERON:0007005!7.28e-07!18;UBERON:0004139!7.28e-07!18;UBERON:0004291!7.28e-07!18|tfbs_overrepresentation_for_novel_motifs=0.795069,0.490989,0.269904,1.58049,0.176699,0.342839,0.425757,0.345089,0.112618,2.24671,0.385334,0.414631,0.106288,0.437133,0.189961,0,0.619876,0.170475,0.096222,1.06389,0.238546,1.20521,0.436294,0.520732,0.758244,2.03716,0.630402,0.361771,0.213277,1.29897,0.349031,0.717576,0.168723,0.570676,0.556756,0.308746,0.161521,0.411296,0.144953,0.391645,0.173534,0.353696,0.255102,0.191571,1.11259,0.856658,1.34233,1.74231,0.208261,0.215702,0.603113,0.488021,0.0612063,0.855661,0.87275,0.443782,0.223087,0.40287,0.60268,0.441884,0.698157,0.496904,0.383763,0.592318,5.19903,0.631188,1.00675,1.3527,0.693631,1.20659,0.253722,0.110167,0.299271,0.905636,0.0810502,0.54852,0.0786324,0.532872,1.63162,0.679143,0.110993,0.636582,0.495545,0.101814,0.792744,0.444993,0.4982,0.0651072,4.58964,1.51408,1.07554,0.797601,0.730003,0.181374,0.141946,0.129056,0.340672,0.732731,1.34284,0.0534645,0.486605,0.717305,0.838603,0.603683,0.602672,0.353298,0.660145,0.372438,8.78026,0.67437,0.286453,0.840348,0.243062,0.390066,1.0825,0.172131,0.337757,0.333247,0.621127,0.158673,0.910937,0.572279,0.464505,0.532013,1.13603,0.685116,0.433317,0.723425,1.00525,1.03388,0.821997,7.52951,0.976125,0.456508,1.10385,0.115066,0.300001,0.35497,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.354106,0.546641,1.84176,0.302077,1.60254,1.8264,0.103135,0.857198,0.133365,0.455644,0.93735,0.488969,0.199652,0.290467,0.299755,1.06466,0.791909,1.63996,0.284483,0.593295,0.448733,1.50123,0.413167,0.935682|tfbs_overrepresentation_jaspar=MA0003.1;0.0832519,MA0004.1;0.330313,MA0006.1;0.547312,MA0007.1;0.316976,MA0009.1;0.743257,MA0014.1;0.919317,MA0017.1;0.598706,MA0019.1;0.567591,MA0024.1;0.70077,MA0025.1;0.971686,MA0027.1;2.37948,MA0028.1;0.567414,MA0029.1;0.679737,MA0030.1;0.686088,MA0031.1;0.651724,MA0038.1;0.462726,MA0040.1;0.755433,MA0041.1;0.263922,MA0042.1;0.252679,MA0043.1;0.837621,MA0046.1;0.778239,MA0048.1;0.054097,MA0050.1;0.365212,MA0051.1;0.471092,MA0052.1;0.76328,MA0055.1;0.0494654,MA0056.1;0,MA0057.1;0.71676,MA0058.1;0.246908,MA0059.1;0.257372,MA0060.1;0.395347,MA0061.1;0.147394,MA0063.1;0,MA0066.1;0.452472,MA0067.1;1.08124,MA0068.1;0.0500842,MA0069.1;0.76361,MA0070.1;0.75417,MA0071.1;0.364454,MA0072.1;0.745922,MA0073.1;0.000531005,MA0074.1;0.419185,MA0076.1;0.635923,MA0077.1;0.724865,MA0078.1;0.502121,MA0081.1;0.277253,MA0083.1;0.836845,MA0084.1;1.4063,MA0087.1;0.794721,MA0088.1;0.28966,MA0089.1;0,MA0090.1;0.299987,MA0091.1;0.342071,MA0092.1;0.300264,MA0093.1;0.20148,MA0095.1;0,MA0098.1;0,MA0100.1;0.408523,MA0101.1;0.265031,MA0103.1;0.216742,MA0105.1;0.0759118,MA0106.1;3.23418,MA0107.1;0.211681,MA0108.2;0.589413,MA0109.1;0,MA0111.1;0.839864,MA0113.1;0.482899,MA0114.1;2.0321,MA0115.1;0.84036,MA0116.1;0.186271,MA0117.1;0.808813,MA0119.1;1.34784,MA0122.1;0.828211,MA0124.1;1.02871,MA0125.1;0.955734,MA0130.1;0,MA0131.1;0.563262,MA0132.1;0,MA0133.1;0,MA0135.1;0.873285,MA0136.1;0.437601,MA0139.1;1.14144,MA0140.1;0.408417,MA0141.1;0.658164,MA0142.1;0.63775,MA0143.1;0.49828,MA0144.1;0.147954,MA0145.1;0.133285,MA0146.1;2.62666,MA0147.1;0.157258,MA0148.1;0.344843,MA0149.1;0.269772,MA0062.2;0.271822,MA0035.2;0.412747,MA0039.2;3.83682,MA0138.2;1.36778,MA0002.2;0.699393,MA0137.2;0.230686,MA0104.2;0.744492,MA0047.2;0.46201,MA0112.2;0.0329566,MA0065.2;1.30208,MA0150.1;0.316876,MA0151.1;0,MA0152.1;0.46211,MA0153.1;0.889592,MA0154.1;0.0529077,MA0155.1;0.637282,MA0156.1;0.222905,MA0157.1;0.606944,MA0158.1;0,MA0159.1;0.165031,MA0160.1;0.918217,MA0161.1;0,MA0162.1;0.103104,MA0163.1;0.0308606,MA0164.1;1.95358,MA0080.2;0.212408,MA0018.2;4.01071,MA0099.2;0.549696,MA0079.2;2.22608,MA0102.2;1.45844,MA0258.1;0.421574,MA0259.1;0.891672,MA0442.1;0}} | ||
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| |||
| | |||
}} | |||
Latest revision as of 15:38, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr10:127774817..127774874,+ | p1@Cs |
| Mm9::chr11:6191663..6191690,+ | p2@Ogdh |
| Mm9::chr4:116230385..116230404,+ | p5@Gpbp1l1 |
| Mm9::chr5:136254498..136254515,+ | p3@Mdh2 |
| Mm9::chr5:136254517..136254533,+ | p1@Mdh2 |
| Mm9::chr5:136254544..136254559,+ | p2@Mdh2 |
| Mm9::chr5:136254570..136254582,+ | p4@Mdh2 |
| Mm9::chr7:104727938..104728011,- | p1@1810020D17Rik |
| Mm9::chr8:42101937..42101968,- | p5@Mtus1 |
| Mm9::chr9:108839183..108839195,- | p@chr9:108839183..108839195 - |
| Mm9::chr9:108839202..108839231,- | p@chr9:108839202..108839231 - |
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:0006096 | glycolysis | 0.000719686101583094 |
| GO:0006007 | glucose catabolic process | 0.000719686101583094 |
| GO:0046365 | monosaccharide catabolic process | 0.000719686101583094 |
| GO:0019320 | hexose catabolic process | 0.000719686101583094 |
| GO:0046164 | alcohol catabolic process | 0.000719686101583094 |
| GO:0044275 | cellular carbohydrate catabolic process | 0.000835044202329801 |
| GO:0016052 | carbohydrate catabolic process | 0.000852708932219754 |
| GO:0006006 | glucose metabolic process | 0.00135788563649404 |
| GO:0005739 | mitochondrion | 0.0017805292280721 |
| GO:0019318 | hexose metabolic process | 0.0017805292280721 |
| GO:0005996 | monosaccharide metabolic process | 0.0017805292280721 |
| GO:0050164 | oxoglutarate dehydrogenase (NADP+) activity | 0.0017805292280721 |
| GO:0004591 | oxoglutarate dehydrogenase (succinyl-transferring) activity | 0.00305216858660128 |
| GO:0004691 | cAMP-dependent protein kinase activity | 0.00305216858660128 |
| GO:0044265 | cellular macromolecule catabolic process | 0.00377011932676117 |
| GO:0030976 | thiamin pyrophosphate binding | 0.00377011932676117 |
| GO:0030060 | L-malate dehydrogenase activity | 0.00377011932676117 |
| GO:0044262 | cellular carbohydrate metabolic process | 0.0039228738921035 |
| GO:0006066 | alcohol metabolic process | 0.0039228738921035 |
| GO:0004690 | cyclic nucleotide-dependent protein kinase activity | 0.0042725677946356 |
| GO:0009057 | macromolecule catabolic process | 0.00468653004588212 |
| GO:0006108 | malate metabolic process | 0.00485492465245523 |
| GO:0005975 | carbohydrate metabolic process | 0.00603378529492736 |
| GO:0016624 | oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor | 0.00622980388168085 |
| GO:0016615 | malate dehydrogenase activity | 0.00683461031047704 |
| GO:0044248 | cellular catabolic process | 0.00711899562963582 |
| GO:0043648 | dicarboxylic acid metabolic process | 0.00711899562963582 |
| GO:0031594 | neuromuscular junction | 0.00991357063876156 |
| GO:0009056 | catabolic process | 0.0106749828994384 |
| GO:0006100 | tricarboxylic acid cycle intermediate metabolic process | 0.0106749828994384 |
| GO:0051969 | regulation of transmission of nerve impulse | 0.0133400725415185 |
| GO:0050804 | regulation of synaptic transmission | 0.0133400725415185 |
| GO:0006099 | tricarboxylic acid cycle | 0.0145990669148224 |
| GO:0046356 | acetyl-CoA catabolic process | 0.0145990669148224 |
| GO:0001707 | mesoderm formation | 0.0145990669148224 |
| GO:0048332 | mesoderm morphogenesis | 0.0145990669148224 |
| GO:0031644 | regulation of neurological process | 0.0145990669148224 |
| GO:0009060 | aerobic respiration | 0.0145990669148224 |
| GO:0001704 | formation of primary germ layer | 0.0147303354289522 |
| GO:0044444 | cytoplasmic part | 0.0147303354289522 |
| GO:0009109 | coenzyme catabolic process | 0.0147303354289522 |
| GO:0016620 | oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor | 0.0147303354289522 |
| GO:0045333 | cellular respiration | 0.0148060594833286 |
| GO:0016491 | oxidoreductase activity | 0.0148060594833286 |
| GO:0051187 | cofactor catabolic process | 0.0151680576498623 |
| GO:0006084 | acetyl-CoA metabolic process | 0.0157639835889618 |
| GO:0016903 | oxidoreductase activity, acting on the aldehyde or oxo group of donors | 0.0172399256059361 |
| GO:0007498 | mesoderm development | 0.0217541713803542 |
| GO:0007369 | gastrulation | 0.0269447198396174 |
| GO:0015980 | energy derivation by oxidation of organic compounds | 0.0281032602653716 |
| GO:0048729 | tissue morphogenesis | 0.0312938817120633 |
| GO:0019842 | vitamin binding | 0.0428982228502034 |
| GO:0016616 | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | 0.0440809510405541 |
| GO:0050662 | coenzyme binding | 0.0456094997535444 |
| GO:0016614 | oxidoreductase activity, acting on CH-OH group of donors | 0.0459307794156284 |
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 |
|---|---|---|
| intestine | 3.00e-11 | 31 |
| mucosa | 2.83e-08 | 15 |
| intestinal mucosa | 3.86e-07 | 13 |
| anatomical wall | 3.86e-07 | 13 |
| wall of intestine | 3.86e-07 | 13 |
| gastrointestinal system mucosa | 3.86e-07 | 13 |
| primary circulatory organ | 7.28e-07 | 18 |
| heart | 7.28e-07 | 18 |
| primitive heart tube | 7.28e-07 | 18 |
| primary heart field | 7.28e-07 | 18 |
| anterior lateral plate mesoderm | 7.28e-07 | 18 |
| heart tube | 7.28e-07 | 18 |
| heart primordium | 7.28e-07 | 18 |
| cardiac mesoderm | 7.28e-07 | 18 |
| cardiogenic plate | 7.28e-07 | 18 |
| heart rudiment | 7.28e-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 | 0.0832519 |
| MA0004.1 | 0.330313 |
| MA0006.1 | 0.547312 |
| MA0007.1 | 0.316976 |
| MA0009.1 | 0.743257 |
| MA0014.1 | 0.919317 |
| MA0017.1 | 0.598706 |
| MA0019.1 | 0.567591 |
| MA0024.1 | 0.70077 |
| MA0025.1 | 0.971686 |
| MA0027.1 | 2.37948 |
| MA0028.1 | 0.567414 |
| MA0029.1 | 0.679737 |
| MA0030.1 | 0.686088 |
| MA0031.1 | 0.651724 |
| MA0038.1 | 0.462726 |
| MA0040.1 | 0.755433 |
| MA0041.1 | 0.263922 |
| MA0042.1 | 0.252679 |
| MA0043.1 | 0.837621 |
| MA0046.1 | 0.778239 |
| MA0048.1 | 0.054097 |
| MA0050.1 | 0.365212 |
| MA0051.1 | 0.471092 |
| MA0052.1 | 0.76328 |
| MA0055.1 | 0.0494654 |
| MA0056.1 | 0 |
| MA0057.1 | 0.71676 |
| MA0058.1 | 0.246908 |
| MA0059.1 | 0.257372 |
| MA0060.1 | 0.395347 |
| MA0061.1 | 0.147394 |
| MA0063.1 | 0 |
| MA0066.1 | 0.452472 |
| MA0067.1 | 1.08124 |
| MA0068.1 | 0.0500842 |
| MA0069.1 | 0.76361 |
| MA0070.1 | 0.75417 |
| MA0071.1 | 0.364454 |
| MA0072.1 | 0.745922 |
| MA0073.1 | 0.000531005 |
| MA0074.1 | 0.419185 |
| MA0076.1 | 0.635923 |
| MA0077.1 | 0.724865 |
| MA0078.1 | 0.502121 |
| MA0081.1 | 0.277253 |
| MA0083.1 | 0.836845 |
| MA0084.1 | 1.4063 |
| MA0087.1 | 0.794721 |
| MA0088.1 | 0.28966 |
| MA0089.1 | 0 |
| MA0090.1 | 0.299987 |
| MA0091.1 | 0.342071 |
| MA0092.1 | 0.300264 |
| MA0093.1 | 0.20148 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.408523 |
| MA0101.1 | 0.265031 |
| MA0103.1 | 0.216742 |
| MA0105.1 | 0.0759118 |
| MA0106.1 | 3.23418 |
| MA0107.1 | 0.211681 |
| MA0108.2 | 0.589413 |
| MA0109.1 | 0 |
| MA0111.1 | 0.839864 |
| MA0113.1 | 0.482899 |
| MA0114.1 | 2.0321 |
| MA0115.1 | 0.84036 |
| MA0116.1 | 0.186271 |
| MA0117.1 | 0.808813 |
| MA0119.1 | 1.34784 |
| MA0122.1 | 0.828211 |
| MA0124.1 | 1.02871 |
| MA0125.1 | 0.955734 |
| MA0130.1 | 0 |
| MA0131.1 | 0.563262 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.873285 |
| MA0136.1 | 0.437601 |
| MA0139.1 | 1.14144 |
| MA0140.1 | 0.408417 |
| MA0141.1 | 0.658164 |
| MA0142.1 | 0.63775 |
| MA0143.1 | 0.49828 |
| MA0144.1 | 0.147954 |
| MA0145.1 | 0.133285 |
| MA0146.1 | 2.62666 |
| MA0147.1 | 0.157258 |
| MA0148.1 | 0.344843 |
| MA0149.1 | 0.269772 |
| MA0062.2 | 0.271822 |
| MA0035.2 | 0.412747 |
| MA0039.2 | 3.83682 |
| MA0138.2 | 1.36778 |
| MA0002.2 | 0.699393 |
| MA0137.2 | 0.230686 |
| MA0104.2 | 0.744492 |
| MA0047.2 | 0.46201 |
| MA0112.2 | 0.0329566 |
| MA0065.2 | 1.30208 |
| MA0150.1 | 0.316876 |
| MA0151.1 | 0 |
| MA0152.1 | 0.46211 |
| MA0153.1 | 0.889592 |
| MA0154.1 | 0.0529077 |
| MA0155.1 | 0.637282 |
| MA0156.1 | 0.222905 |
| MA0157.1 | 0.606944 |
| MA0158.1 | 0 |
| MA0159.1 | 0.165031 |
| MA0160.1 | 0.918217 |
| MA0161.1 | 0 |
| MA0162.1 | 0.103104 |
| MA0163.1 | 0.0308606 |
| MA0164.1 | 1.95358 |
| MA0080.2 | 0.212408 |
| MA0018.2 | 4.01071 |
| MA0099.2 | 0.549696 |
| MA0079.2 | 2.22608 |
| MA0102.2 | 1.45844 |
| MA0258.1 | 0.421574 |
| MA0259.1 | 0.891672 |
| MA0442.1 | 0 |
