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MCL coexpression mm9:3147: Difference between revisions

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{{MCL_coexpression_mm9
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cell development;0.00802015991679228;15488!GO:0016829;lyase activity;0.00802015991679228;11428,15488!GO:0060008;Sertoli cell differentiation;0.00802015991679228;15488!GO:0030350;iron-responsive element binding;0.00802015991679228;11428!GO:0003994;aconitate hydratase activity;0.00802015991679228;11428!GO:0003857;3-hydroxyacyl-CoA dehydrogenase activity;0.0133654684857832;15488!GO:0005498;sterol carrier activity;0.0143193601837251;15488!GO:0000038;very-long-chain fatty acid metabolic process;0.0150345043694134;15488!GO:0006635;fatty acid beta-oxidation;0.0261125941469408;15488!GO:0032934;sterol binding;0.0261125941469408;15488!GO:0008584;male gonad development;0.0261125941469408;15488!GO:0051539;4 iron, 4 sulfur cluster binding;0.0261125941469408;11428!GO:0019395;fatty acid oxidation;0.0261125941469408;15488!GO:0046546;development of primary male sexual characteristics;0.0261125941469408;15488!GO:0055072;iron ion homeostasis;0.0261125941469408;11428!GO:0006099;tricarboxylic acid cycle;0.0261125941469408;11428!GO:0006879;cellular iron ion homeostasis;0.0261125941469408;11428!GO:0046356;acetyl-CoA catabolic process;0.0261125941469408;11428!GO:0009060;aerobic respiration;0.0261125941469408;11428!GO:0046661;male sex differentiation;0.0261125941469408;15488!GO:0009109;coenzyme catabolic process;0.0261125941469408;11428!GO:0045333;cellular respiration;0.0261125941469408;11428!GO:0003729;mRNA binding;0.0261125941469408;11428!GO:0051187;cofactor catabolic process;0.0266899475954307;11428!GO:0006084;acetyl-CoA metabolic process;0.0272207618157703;11428!GO:0051536;iron-sulfur cluster binding;0.031860439234296;11428!GO:0051540;metal cluster binding;0.031860439234296;11428!GO:0005496;steroid binding;0.0335731150194027;15488!GO:0016836;hydro-lyase activity;0.033791094855001;11428!GO:0008406;gonad development;0.0339942505142106;15488!GO:0048608;reproductive structure development;0.0341840166258144;15488!GO:0045137;development of primary sexual 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|gostat_on_MCL_coexpression=GO:0060009;Sertoli cell development;0.00802015991679228;15488!GO:0016829;lyase activity;0.00802015991679228;11428,15488!GO:0060008;Sertoli cell differentiation;0.00802015991679228;15488!GO:0030350;iron-responsive element binding;0.00802015991679228;11428!GO:0003994;aconitate hydratase activity;0.00802015991679228;11428!GO:0003857;3-hydroxyacyl-CoA dehydrogenase activity;0.0133654684857832;15488!GO:0005498;sterol carrier activity;0.0143193601837251;15488!GO:0000038;very-long-chain fatty acid metabolic process;0.0150345043694134;15488!GO:0006635;fatty acid beta-oxidation;0.0261125941469408;15488!GO:0032934;sterol binding;0.0261125941469408;15488!GO:0008584;male gonad development;0.0261125941469408;15488!GO:0051539;4 iron, 4 sulfur cluster binding;0.0261125941469408;11428!GO:0019395;fatty acid oxidation;0.0261125941469408;15488!GO:0046546;development of primary male sexual characteristics;0.0261125941469408;15488!GO:0055072;iron ion homeostasis;0.0261125941469408;11428!GO:0006099;tricarboxylic acid cycle;0.0261125941469408;11428!GO:0006879;cellular iron ion homeostasis;0.0261125941469408;11428!GO:0046356;acetyl-CoA catabolic process;0.0261125941469408;11428!GO:0009060;aerobic respiration;0.0261125941469408;11428!GO:0046661;male sex differentiation;0.0261125941469408;15488!GO:0009109;coenzyme catabolic process;0.0261125941469408;11428!GO:0045333;cellular respiration;0.0261125941469408;11428!GO:0003729;mRNA binding;0.0261125941469408;11428!GO:0051187;cofactor catabolic process;0.0266899475954307;11428!GO:0006084;acetyl-CoA metabolic process;0.0272207618157703;11428!GO:0051536;iron-sulfur cluster binding;0.031860439234296;11428!GO:0051540;metal cluster binding;0.031860439234296;11428!GO:0005496;steroid binding;0.0335731150194027;15488!GO:0016836;hydro-lyase activity;0.033791094855001;11428!GO:0008406;gonad development;0.0339942505142106;15488!GO:0048608;reproductive structure development;0.0341840166258144;15488!GO:0045137;development of primary sexual characteristics;0.0357358465760238;15488!GO:0016835;carbon-oxygen lyase activity;0.0357358465760238;11428!GO:0015980;energy derivation by oxidation of organic compounds;0.0387850424476847;11428!GO:0007548;sex differentiation;0.0416569334533002;15488!GO:0003006;reproductive developmental process;0.0462140591944883;15488!GO:0042579;microbody;0.0462140591944883;15488!GO:0005777;peroxisome;0.0462140591944883;15488!GO:0030005;cellular di-, tri-valent inorganic cation homeostasis;0.0485922714011397;11428!GO:0055066;di-, tri-valent inorganic cation homeostasis;0.0488655484476814;11428!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000160!2.79e-11!31;UBERON:0000477!4.81e-08!244;UBERON:0000922!1.78e-07!320
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.193418,0.722405,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.66329,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.756749,0.932027,0.585919,0.731217,0.963352,1.1146,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,0.444545,0.563758,0.902078,0.536514,0.50014,0.582863,0.831295,0.261619,0.610669,1.47707,0.788421,1.05665,0.859154,0.235354,0.646474,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,1.23806,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.777706,1.44925,1.07031,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.181575,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,1.1471,1.88801,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,0.999018,0.721422,1.39822,2.21624,0.954936,1.48249,0.993889,0.622823,0.749933,0.762177,1.61484,1.32889,1.21423,0.741984,1.11251,0.94678,0.562367,0.904334,0.421338
|tfbs_overrepresentation_jaspar=MA0003.1;0.526413,MA0004.1;0.801718,MA0006.1;0.60285,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;0.416365,MA0017.1;0.635031,MA0019.1;1.08369,MA0024.1;1.23079,MA0025.1;1.51835,MA0027.1;2.9431,MA0028.1;1.49373,MA0029.1;1.20789,MA0030.1;1.21482,MA0031.1;1.17722,MA0038.1;0.963265,MA0040.1;1.28983,MA0041.1;0.714279,MA0042.1;0.69885,MA0043.1;1.3775,MA0046.1;1.31428,MA0048.1;1.66457,MA0050.1;0.845669,MA0051.1;0.973068,MA0052.1;1.29825,MA0055.1;1.06076,MA0056.1;0,MA0057.1;0.337566,MA0058.1;0.690848,MA0059.1;0.705317,MA0060.1;0.502699,MA0061.1;0.5406,MA0063.1;0,MA0066.1;0.951196,MA0067.1;1.63197,MA0068.1;0.343188,MA0069.1;1.29861,MA0070.1;1.28847,MA0071.1;0.844726,MA0072.1;1.2796,MA0073.1;0.00834468,MA0074.1;0.911576,MA0076.1;2.67392,MA0077.1;1.2569,MA0078.1;1.0091,MA0081.1;0.732313,MA0083.1;1.37668,MA0084.1;1.96428,MA0087.1;1.33189,MA0088.1;0.27999,MA0089.1;0,MA0090.1;0.762482,MA0091.1;0.816659,MA0092.1;0.762845,MA0093.1;0.62555,MA0095.1;0,MA0098.1;0,MA0100.1;0.89873,MA0101.1;0.71579,MA0103.1;0.647985,MA0105.1;0.405648,MA0106.1;1.01755,MA0107.1;0.640607,MA0108.2;1.10817,MA0109.1;0,MA0111.1;0.778753,MA0113.1;0.986839,MA0114.1;0.537669,MA0115.1;1.38041,MA0116.1;0.602598,MA0117.1;1.34691,MA0119.1;0.716476,MA0122.1;1.36752,MA0124.1;1.57762,MA0125.1;1.5017,MA0130.1;0,MA0131.1;1.07881,MA0132.1;0,MA0133.1;0,MA0135.1;1.4152,MA0136.1;0.933582,MA0139.1;0.462282,MA0140.1;0.898603,MA0141.1;0.671467,MA0142.1;1.16183,MA0143.1;1.00467,MA0144.1;0.541532,MA0145.1;1.44606,MA0146.1;0.900029,MA0147.1;0.556853,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;2.79231,MA0035.2;0.903829,MA0039.2;0.40695,MA0138.2;1.07027,MA0002.2;0.466067,MA0137.2;0.668025,MA0104.2;0.48458,MA0047.2;0.962424,MA0112.2;0.29236,MA0065.2;0.292912,MA0150.1;0.784464,MA0151.1;0,MA0152.1;0.962542,MA0153.1;1.43238,MA0154.1;0.35067,MA0155.1;0.312898,MA0156.1;0.656895,MA0157.1;1.12772,MA0158.1;0,MA0159.1;0.569393,MA0160.1;0.823568,MA0161.1;0,MA0162.1;0.166722,MA0163.1;0.157796,MA0164.1;0.933981,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;0.288542,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0
}}

Latest revision as of 19:39, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr18:50287865..50287921,+p1@Hsd17b4
Mm9::chr4:40090401..40090477,+p1@Aco1
Mm9::chr9:55056747..55056796,+p1@Fbxo22


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:0060009Sertoli cell development0.00802015991679228
GO:0016829lyase activity0.00802015991679228
GO:0060008Sertoli cell differentiation0.00802015991679228
GO:0030350iron-responsive element binding0.00802015991679228
GO:0003994aconitate hydratase activity0.00802015991679228
GO:00038573-hydroxyacyl-CoA dehydrogenase activity0.0133654684857832
GO:0005498sterol carrier activity0.0143193601837251
GO:0000038very-long-chain fatty acid metabolic process0.0150345043694134
GO:0006635fatty acid beta-oxidation0.0261125941469408
GO:0032934sterol binding0.0261125941469408
GO:0008584male gonad development0.0261125941469408
GO:00515394 iron, 4 sulfur cluster binding0.0261125941469408
GO:0019395fatty acid oxidation0.0261125941469408
GO:0046546development of primary male sexual characteristics0.0261125941469408
GO:0055072iron ion homeostasis0.0261125941469408
GO:0006099tricarboxylic acid cycle0.0261125941469408
GO:0006879cellular iron ion homeostasis0.0261125941469408
GO:0046356acetyl-CoA catabolic process0.0261125941469408
GO:0009060aerobic respiration0.0261125941469408
GO:0046661male sex differentiation0.0261125941469408
GO:0009109coenzyme catabolic process0.0261125941469408
GO:0045333cellular respiration0.0261125941469408
GO:0003729mRNA binding0.0261125941469408
GO:0051187cofactor catabolic process0.0266899475954307
GO:0006084acetyl-CoA metabolic process0.0272207618157703
GO:0051536iron-sulfur cluster binding0.031860439234296
GO:0051540metal cluster binding0.031860439234296
GO:0005496steroid binding0.0335731150194027
GO:0016836hydro-lyase activity0.033791094855001
GO:0008406gonad development0.0339942505142106
GO:0048608reproductive structure development0.0341840166258144
GO:0045137development of primary sexual characteristics0.0357358465760238
GO:0016835carbon-oxygen lyase activity0.0357358465760238
GO:0015980energy derivation by oxidation of organic compounds0.0387850424476847
GO:0007548sex differentiation0.0416569334533002
GO:0003006reproductive developmental process0.0462140591944883
GO:0042579microbody0.0462140591944883
GO:0005777peroxisome0.0462140591944883
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0485922714011397
GO:0055066di-, tri-valent inorganic cation homeostasis0.0488655484476814



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
intestine2.79e-1131
anatomical cluster4.81e-08244
embryo1.78e-07320


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)
MA0003.10.526413
MA0004.10.801718
MA0006.10.60285
MA0007.10.784593
MA0009.11.27673
MA0014.10.416365
MA0017.10.635031
MA0019.11.08369
MA0024.11.23079
MA0025.11.51835
MA0027.12.9431
MA0028.11.49373
MA0029.11.20789
MA0030.11.21482
MA0031.11.17722
MA0038.10.963265
MA0040.11.28983
MA0041.10.714279
MA0042.10.69885
MA0043.11.3775
MA0046.11.31428
MA0048.11.66457
MA0050.10.845669
MA0051.10.973068
MA0052.11.29825
MA0055.11.06076
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.10.705317
MA0060.10.502699
MA0061.10.5406
MA0063.10
MA0066.10.951196
MA0067.11.63197
MA0068.10.343188
MA0069.11.29861
MA0070.11.28847
MA0071.10.844726
MA0072.11.2796
MA0073.10.00834468
MA0074.10.911576
MA0076.12.67392
MA0077.11.2569
MA0078.11.0091
MA0081.10.732313
MA0083.11.37668
MA0084.11.96428
MA0087.11.33189
MA0088.10.27999
MA0089.10
MA0090.10.762482
MA0091.10.816659
MA0092.10.762845
MA0093.10.62555
MA0095.10
MA0098.10
MA0100.10.89873
MA0101.10.71579
MA0103.10.647985
MA0105.10.405648
MA0106.11.01755
MA0107.10.640607
MA0108.21.10817
MA0109.10
MA0111.10.778753
MA0113.10.986839
MA0114.10.537669
MA0115.11.38041
MA0116.10.602598
MA0117.11.34691
MA0119.10.716476
MA0122.11.36752
MA0124.11.57762
MA0125.11.5017
MA0130.10
MA0131.11.07881
MA0132.10
MA0133.10
MA0135.11.4152
MA0136.10.933582
MA0139.10.462282
MA0140.10.898603
MA0141.10.671467
MA0142.11.16183
MA0143.11.00467
MA0144.10.541532
MA0145.11.44606
MA0146.10.900029
MA0147.10.556853
MA0148.10.820161
MA0149.10.722227
MA0062.22.79231
MA0035.20.903829
MA0039.20.40695
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.20.48458
MA0047.20.962424
MA0112.20.29236
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.35067
MA0155.10.312898
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.166722
MA0163.10.157796
MA0164.10.933981
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.20.288542
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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