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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 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|gostat_on_MCL_coexpression=GO:0005201;extracellular 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 IDGO nameFDR corrected p-value
GO:0005201extracellular matrix structural constituent1.28016208344516e-05
GO:0044420extracellular matrix part1.2828163433318e-05
GO:0005587collagen type IV1.2828163433318e-05
GO:0030935sheet-forming collagen1.2828163433318e-05
GO:0005578proteinaceous extracellular matrix0.000231088263798871
GO:0030020extracellular matrix structural constituent conferring tensile strength0.000231088263798871
GO:0005581collagen0.000290155949761186
GO:0005604basement membrane0.000805297147187118
GO:0006817phosphate transport0.000836646297554101
GO:0044421extracellular region part0.00162256709454504
GO:0015698inorganic anion transport0.00299634711228363
GO:0006820anion transport0.00385854729848647
GO:0001527microfibril0.00800448178953245
GO:0043205fibril0.00891854667042571
GO:0005021vascular endothelial growth factor receptor activity0.0138687345289946
GO:0005615extracellular space0.0274070605332511
GO:0022610biological adhesion0.031419874086069
GO:0007155cell adhesion0.031419874086069
GO:0050730regulation of peptidyl-tyrosine phosphorylation0.0371532336198108
GO:0006811ion transport0.0388729510970686
GO:0001932regulation of protein amino acid phosphorylation0.0414491607461372
GO:0033238regulation of amine metabolic process0.0414491607461372
GO:0006521regulation of amino acid metabolic process0.0414491607461372
GO:0018212peptidyl-tyrosine modification0.0414491607461372
GO:0042325regulation of phosphorylation0.0414491607461372
GO:0018108peptidyl-tyrosine phosphorylation0.0414491607461372
GO:0051174regulation of phosphorus metabolic process0.0414491607461372
GO:0019220regulation of phosphate metabolic process0.0414491607461372
GO:0004714transmembrane receptor protein tyrosine kinase activity0.0442858686454993



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>

Uber Anatomy
Ontology termp-valuen
primary circulatory organ1.07e-0818
heart1.07e-0818
primitive heart tube1.07e-0818
primary heart field1.07e-0818
anterior lateral plate mesoderm1.07e-0818
heart tube1.07e-0818
heart primordium1.07e-0818
cardiac mesoderm1.07e-0818
cardiogenic plate1.07e-0818
heart rudiment1.07e-0818
compound organ2.50e-0743
lung6.17e-0714
respiratory tube6.17e-0714
respiration organ6.17e-0714
pair of lungs6.17e-0714
lung primordium6.17e-0714
lung bud6.17e-0714
splanchnic layer of lateral plate mesoderm6.35e-0733


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)
MA0003.10.662116
MA0004.10.394951
MA0006.10.238555
MA0007.10.38073
MA0009.10.82278
MA0014.10.248772
MA0017.10.26239
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.10.24786
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.323687
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.10.589612
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.0882028
MA0056.10
MA0057.10.258928
MA0058.10.305206
MA0059.10.316585
MA0060.10.505012
MA0061.10.194456
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.077274
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.10.126434
MA0074.11.22546
MA0076.10.279739
MA0077.10.804033
MA0078.10.575205
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.728131
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.95209
MA0093.10.2553
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.324888
MA0103.10.272167
MA0105.10.720048
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.19245
MA0115.10.921497
MA0116.11.93347
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.441109
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.11.17902
MA0146.10.0548413
MA0147.10.205697
MA0148.10.410398
MA0149.10.330018
MA0062.20.113962
MA0035.20.482026
MA0039.20.0156581
MA0138.20.630612
MA0002.21.41154
MA0137.20.287486
MA0104.20.157347
MA0047.20.533516
MA0112.20.442124
MA0065.20.773848
MA0150.10.991233
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.581988
MA0155.10.490492
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.10.176565
MA0163.10.321031
MA0164.11.26737
MA0080.20.267388
MA0018.20.51781
MA0099.20.624421
MA0079.20.0340753
MA0102.21.5442
MA0258.10.533988
MA0259.10.196451
MA0442.10
Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=MCL_coexpression_mm9:837&oldid=3072836"