MCL coexpression mm9:837: Difference between revisions
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{{MCL_coexpression_mm9| | 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matrix structural constituent;1.28016208344516e-05;14118,12826,12827!GO:0044420;extracellular matrix part;1.2828163433318e-05;14118,12826,12827!GO:0005587;collagen type IV;1.2828163433318e-05;12826,12827!GO:0030935;sheet-forming collagen;1.2828163433318e-05;12826,12827!GO:0005578;proteinaceous extracellular matrix;0.000231088263798871;14118,12826,12827!GO:0030020;extracellular matrix structural constituent conferring tensile strength;0.000231088263798871;12826,12827!GO:0005581;collagen;0.000290155949761186;12826,12827!GO:0005604;basement membrane;0.000805297147187118;12826,12827!GO:0006817;phosphate transport;0.000836646297554101;12826,12827!GO:0044421;extracellular region part;0.00162256709454504;18596,14118,12826,12827!GO:0015698;inorganic anion transport;0.00299634711228363;12826,12827!GO:0006820;anion transport;0.00385854729848647;12826,12827!GO:0001527;microfibril;0.00800448178953245;14118!GO:0043205;fibril;0.00891854667042571;14118!GO:0005021;vascular endothelial growth factor receptor activity;0.0138687345289946;18596!GO:0005615;extracellular space;0.0274070605332511;18596,12826,12827!GO:0022610;biological adhesion;0.031419874086069;12826,12827!GO:0007155;cell adhesion;0.031419874086069;12826,12827!GO:0050730;regulation of peptidyl-tyrosine phosphorylation;0.0371532336198108;18596!GO:0006811;ion transport;0.0388729510970686;12826,12827!GO:0001932;regulation of protein amino acid phosphorylation;0.0414491607461372;18596!GO:0033238;regulation of amine metabolic process;0.0414491607461372;18596!GO:0006521;regulation of amino acid metabolic process;0.0414491607461372;18596!GO:0018212;peptidyl-tyrosine modification;0.0414491607461372;18596!GO:0042325;regulation of phosphorylation;0.0414491607461372;18596!GO:0018108;peptidyl-tyrosine phosphorylation;0.0414491607461372;18596!GO:0051174;regulation of phosphorus metabolic process;0.0414491607461372;18596!GO:0019220;regulation of phosphate metabolic process;0.0414491607461372;18596!GO:0004714;transmembrane receptor protein tyrosine kinase activity;0.0442858686454993;18596!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0007100!1.07e-08!18;UBERON:0000948!1.07e-08!18;UBERON:0005498!1.07e-08!18;UBERON:0004140!1.07e-08!18;UBERON:0009881!1.07e-08!18;UBERON:0004141!1.07e-08!18;UBERON:0003084!1.07e-08!18;UBERON:0007005!1.07e-08!18;UBERON:0004139!1.07e-08!18;UBERON:0004291!1.07e-08!18;UBERON:0003103!2.50e-07!43;UBERON:0002048!6.17e-07!14;UBERON:0000117!6.17e-07!14;UBERON:0000171!6.17e-07!14;UBERON:0000170!6.17e-07!14;UBERON:0005597!6.17e-07!14;UBERON:0000118!6.17e-07!14;UBERON:0004872!6.35e-07!33|tfbs_overrepresentation_for_novel_motifs=0.93395,0.227469,0.330161,0.394491,0.227651,0.40827,0.495658,0.880357,0.154135,0.573183,0.453212,0.484001,0.88117,0.507558,0.24249,0,0.696644,0.62892,0.829774,0.528436,0.296085,0.179861,0.50668,0.64218,0.337218,1.32254,0.402559,0.428336,0.739731,1.09271,0.414842,0.796599,0.624261,0.364174,0.242923,0.482999,0.210533,0.480503,1.06548,0.167387,0.637027,0.419787,1.03041,0.244285,1.14242,0.383899,0.618203,0.443479,0.904531,0.745859,1.62723,0.560572,0.30602,0.937018,0.954342,0.514504,0.279148,0.471658,0.384731,0.512521,0.776777,0.569793,0.492158,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,1.51902,0.151245,0.424998,0.987652,0.748687,0.107966,0.113315,0.607043,0.759798,0.299972,0.152219,0.713779,0.568383,0.858535,0.873141,1.33784,0.439624,0.319367,0.623015,1.60001,1.15927,0.878077,0.809272,0.657661,0.188213,0.17334,0.14449,0.812053,0.618454,0.0816605,0.210602,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,0.439611,0.30446,0.297733,0.919252,0.921485,0.814064,0.458194,1.16629,0.222515,1.15833,0.398075,0.697928,0.597328,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.663857,0.90286,1.00644,1.05894,0.527782,1.18781,0.0467191,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,0.364791,0.649035,0.32395,0.041769,0.938577,0.527659,0.526881,1.01974,0.561556,0.253271,0.928824,0.362302,1.1483,0.872292,0.763895,0.345891,0.669337,0.519673,0.209556,0.482466,0.683949|tfbs_overrepresentation_jaspar=MA0003.1;0.662116,MA0004.1;0.394951,MA0006.1;0.238555,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;0.589612,MA0050.1;0.431976,MA0051.1;0.542972,MA0052.1;0.84317,MA0055.1;0.0882028,MA0056.1;0,MA0057.1;0.258928,MA0058.1;0.305206,MA0059.1;0.316585,MA0060.1;0.505012,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;0.833895,MA0071.1;0.431174,MA0072.1;0.825495,MA0073.1;0.126434,MA0074.1;1.22546,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;0.728131,MA0089.1;0,MA0090.1;0.362551,MA0091.1;0.407455,MA0092.1;0.95209,MA0093.1;0.2553,MA0095.1;0,MA0098.1;0,MA0100.1;0.477594,MA0101.1;0.324888,MA0103.1;0.272167,MA0105.1;0.720048,MA0106.1;0.582805,MA0107.1;0.266586,MA0108.2;0.665343,MA0109.1;0,MA0111.1;0.375908,MA0113.1;0.555251,MA0114.1;0.19245,MA0115.1;0.921497,MA0116.1;1.93347,MA0117.1;0.88947,MA0119.1;0.325434,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;0.441109,MA0140.1;0.477483,MA0141.1;0.29014,MA0142.1;0.714976,MA0143.1;0.571221,MA0144.1;0.195095,MA0145.1;1.17902,MA0146.1;0.0548413,MA0147.1;0.205697,MA0148.1;0.410398,MA0149.1;0.330018,MA0062.2;0.113962,MA0035.2;0.482026,MA0039.2;0.0156581,MA0138.2;0.630612,MA0002.2;1.41154,MA0137.2;0.287486,MA0104.2;0.157347,MA0047.2;0.533516,MA0112.2;0.442124,MA0065.2;0.773848,MA0150.1;0.991233,MA0151.1;0,MA0152.1;0.53362,MA0153.1;0.971406,MA0154.1;0.581988,MA0155.1;0.490492,MA0156.1;0.278949,MA0157.1;0.683365,MA0158.1;0,MA0159.1;0.214506,MA0160.1;0.413266,MA0161.1;0,MA0162.1;0.176565,MA0163.1;0.321031,MA0164.1;1.26737,MA0080.2;0.267388,MA0018.2;0.51781,MA0099.2;0.624421,MA0079.2;0.0340753,MA0102.2;1.5442,MA0258.1;0.533988,MA0259.1;0.196451,MA0442.1;0}} | ||
Latest revision as of 15:58, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr18:61204957..61204967,+ | p4@Pdgfrb |
| Mm9::chr2:125127459..125127472,- | p@chr2:125127459..125127472 - |
| Mm9::chr8:11199340..11199353,- | p@chr8:11199340..11199353 - |
| Mm9::chr8:11219189..11219201,- | p@chr8:11219189..11219201 - |
| Mm9::chr8:11312731..11312758,- | p1@Col4a1 |
| Mm9::chr8:11312869..11312887,+ | p1@Col4a2 |
| Mm9::chr8:11354301..11354323,- | p@chr8:11354301..11354323 - |
| Mm9::chr8:11448495..11448557,+ | p@chr8:11448495..11448557 + |
| Mm9::chr8:11448969..11449001,+ | p@chr8:11448969..11449001 + |
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:0005201 | extracellular matrix structural constituent | 1.28016208344516e-05 |
| GO:0044420 | extracellular matrix part | 1.2828163433318e-05 |
| GO:0005587 | collagen type IV | 1.2828163433318e-05 |
| GO:0030935 | sheet-forming collagen | 1.2828163433318e-05 |
| GO:0005578 | proteinaceous extracellular matrix | 0.000231088263798871 |
| GO:0030020 | extracellular matrix structural constituent conferring tensile strength | 0.000231088263798871 |
| GO:0005581 | collagen | 0.000290155949761186 |
| GO:0005604 | basement membrane | 0.000805297147187118 |
| GO:0006817 | phosphate transport | 0.000836646297554101 |
| GO:0044421 | extracellular region part | 0.00162256709454504 |
| GO:0015698 | inorganic anion transport | 0.00299634711228363 |
| GO:0006820 | anion transport | 0.00385854729848647 |
| GO:0001527 | microfibril | 0.00800448178953245 |
| GO:0043205 | fibril | 0.00891854667042571 |
| GO:0005021 | vascular endothelial growth factor receptor activity | 0.0138687345289946 |
| GO:0005615 | extracellular space | 0.0274070605332511 |
| GO:0022610 | biological adhesion | 0.031419874086069 |
| GO:0007155 | cell adhesion | 0.031419874086069 |
| GO:0050730 | regulation of peptidyl-tyrosine phosphorylation | 0.0371532336198108 |
| GO:0006811 | ion transport | 0.0388729510970686 |
| GO:0001932 | regulation of protein amino acid phosphorylation | 0.0414491607461372 |
| GO:0033238 | regulation of amine metabolic process | 0.0414491607461372 |
| GO:0006521 | regulation of amino acid metabolic process | 0.0414491607461372 |
| GO:0018212 | peptidyl-tyrosine modification | 0.0414491607461372 |
| GO:0042325 | regulation of phosphorylation | 0.0414491607461372 |
| GO:0018108 | peptidyl-tyrosine phosphorylation | 0.0414491607461372 |
| GO:0051174 | regulation of phosphorus metabolic process | 0.0414491607461372 |
| GO:0019220 | regulation of phosphate metabolic process | 0.0414491607461372 |
| GO:0004714 | transmembrane receptor protein tyrosine kinase activity | 0.0442858686454993 |
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 |
|---|---|---|
| primary circulatory organ | 1.07e-08 | 18 |
| heart | 1.07e-08 | 18 |
| primitive heart tube | 1.07e-08 | 18 |
| primary heart field | 1.07e-08 | 18 |
| anterior lateral plate mesoderm | 1.07e-08 | 18 |
| heart tube | 1.07e-08 | 18 |
| heart primordium | 1.07e-08 | 18 |
| cardiac mesoderm | 1.07e-08 | 18 |
| cardiogenic plate | 1.07e-08 | 18 |
| heart rudiment | 1.07e-08 | 18 |
| compound organ | 2.50e-07 | 43 |
| lung | 6.17e-07 | 14 |
| respiratory tube | 6.17e-07 | 14 |
| respiration organ | 6.17e-07 | 14 |
| pair of lungs | 6.17e-07 | 14 |
| lung primordium | 6.17e-07 | 14 |
| lung bud | 6.17e-07 | 14 |
| splanchnic layer of lateral plate mesoderm | 6.35e-07 | 33 |
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 | 0.238555 |
| 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 | 0.589612 |
| MA0050.1 | 0.431976 |
| MA0051.1 | 0.542972 |
| MA0052.1 | 0.84317 |
| MA0055.1 | 0.0882028 |
| MA0056.1 | 0 |
| MA0057.1 | 0.258928 |
| MA0058.1 | 0.305206 |
| MA0059.1 | 0.316585 |
| MA0060.1 | 0.505012 |
| 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 | 0.833895 |
| MA0071.1 | 0.431174 |
| MA0072.1 | 0.825495 |
| MA0073.1 | 0.126434 |
| MA0074.1 | 1.22546 |
| 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 | 0.728131 |
| MA0089.1 | 0 |
| MA0090.1 | 0.362551 |
| MA0091.1 | 0.407455 |
| MA0092.1 | 0.95209 |
| MA0093.1 | 0.2553 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.477594 |
| MA0101.1 | 0.324888 |
| MA0103.1 | 0.272167 |
| MA0105.1 | 0.720048 |
| MA0106.1 | 0.582805 |
| MA0107.1 | 0.266586 |
| MA0108.2 | 0.665343 |
| MA0109.1 | 0 |
| MA0111.1 | 0.375908 |
| MA0113.1 | 0.555251 |
| MA0114.1 | 0.19245 |
| MA0115.1 | 0.921497 |
| MA0116.1 | 1.93347 |
| MA0117.1 | 0.88947 |
| MA0119.1 | 0.325434 |
| 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 | 0.441109 |
| MA0140.1 | 0.477483 |
| MA0141.1 | 0.29014 |
| MA0142.1 | 0.714976 |
| MA0143.1 | 0.571221 |
| MA0144.1 | 0.195095 |
| MA0145.1 | 1.17902 |
| MA0146.1 | 0.0548413 |
| MA0147.1 | 0.205697 |
| MA0148.1 | 0.410398 |
| MA0149.1 | 0.330018 |
| MA0062.2 | 0.113962 |
| MA0035.2 | 0.482026 |
| MA0039.2 | 0.0156581 |
| MA0138.2 | 0.630612 |
| MA0002.2 | 1.41154 |
| MA0137.2 | 0.287486 |
| MA0104.2 | 0.157347 |
| MA0047.2 | 0.533516 |
| MA0112.2 | 0.442124 |
| MA0065.2 | 0.773848 |
| MA0150.1 | 0.991233 |
| MA0151.1 | 0 |
| MA0152.1 | 0.53362 |
| MA0153.1 | 0.971406 |
| MA0154.1 | 0.581988 |
| MA0155.1 | 0.490492 |
| MA0156.1 | 0.278949 |
| MA0157.1 | 0.683365 |
| MA0158.1 | 0 |
| MA0159.1 | 0.214506 |
| MA0160.1 | 0.413266 |
| MA0161.1 | 0 |
| MA0162.1 | 0.176565 |
| MA0163.1 | 0.321031 |
| MA0164.1 | 1.26737 |
| MA0080.2 | 0.267388 |
| MA0018.2 | 0.51781 |
| MA0099.2 | 0.624421 |
| MA0079.2 | 0.0340753 |
| MA0102.2 | 1.5442 |
| MA0258.1 | 0.533988 |
| MA0259.1 | 0.196451 |
| MA0442.1 | 0 |
