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MCL coexpression mm9:818: Difference between revisions

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{{MCL_coexpression_mm9
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metabolic process;0.00921864035950844;28200,17117!GO:0008111;alpha-methylacyl-CoA racemase activity;0.0107482502539566;17117!GO:0006545;glycine biosynthetic process;0.0107482502539566;13361!GO:0004371;glycerone kinase activity;0.0107482502539566;225913!GO:0004146;dihydrofolate reductase activity;0.0107482502539566;13361!GO:0008300;isoprenoid catabolic process;0.0107482502539566;17117!GO:0042579;microbody;0.0107482502539566;28200,17117!GO:0005777;peroxisome;0.0107482502539566;28200,17117!GO:0003994;aconitate hydratase activity;0.0135507654932865;11428!GO:0030350;iron-responsive element binding;0.0135507654932865;11428!GO:0050662;coenzyme binding;0.0135507654932865;226564,13361!GO:0004995;tachykinin receptor activity;0.0173476077320651;21336!GO:0016829;lyase activity;0.0182546376454438;11428,225913!GO:0001758;retinal dehydrogenase activity;0.0182546376454438;28200!GO:0004090;carbonyl reductase (NADPH) activity;0.0182546376454438;28200!GO:0048037;cofactor binding;0.0182546376454438;226564,13361!GO:0043288;apocarotenoid metabolic process;0.0182546376454438;28200!GO:0042574;retinal metabolic process;0.0182546376454438;28200!GO:0004499;flavin-containing monooxygenase activity;0.0182546376454438;226564!GO:0016491;oxidoreductase activity;0.0198160634969006;226564,13361,28200!GO:0009070;serine family amino acid biosynthetic process;0.0198160634969006;13361!GO:0006544;glycine metabolic process;0.0252121552214093;13361!GO:0050661;NADP binding;0.029694797603961;13361!GO:0016646;oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor;0.029694797603961;13361!GO:0016854;racemase and epimerase activity;0.029694797603961;17117!GO:0048265;response to pain;0.029694797603961;21336!GO:0016101;diterpenoid metabolic process;0.029694797603961;28200!GO:0001523;retinoid metabolic process;0.029694797603961;28200!GO:0006721;terpenoid metabolic process;0.0334383196327042;28200!GO:0006776;vitamin A metabolic process;0.0369292419083422;28200!GO:0009069;serine family amino acid metabolic process;0.0379653600349381;13361!GO:0051539;4 iron, 4 sulfur cluster binding;0.0395410453392476;11428!GO:0006071;glycerol metabolic process;0.0395410453392476;225913!GO:0019751;polyol metabolic process;0.0395410453392476;225913!GO:0016645;oxidoreductase activity, acting on the CH-NH group of donors;0.0395410453392476;13361!GO:0006775;fat-soluble vitamin metabolic process;0.0399409936252014;28200!GO:0016709;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen;0.0399409936252014;226564!GO:0006099;tricarboxylic acid cycle;0.0399409936252014;11428!GO:0055072;iron ion homeostasis;0.0399409936252014;11428!GO:0006879;cellular iron ion homeostasis;0.0399409936252014;11428!GO:0033555;multicellular organismal response to stress;0.0399409936252014;21336!GO:0046356;acetyl-CoA catabolic process;0.0399409936252014;11428!GO:0044248;cellular catabolic process;0.0399409936252014;11428,17117!GO:0006091;generation of precursor metabolites and energy;0.0399409936252014;226564,11428!GO:0009060;aerobic respiration;0.0399409936252014;11428!GO:0044242;cellular lipid catabolic process;0.0414499359845858;17117!GO:0009109;coenzyme catabolic process;0.0414499359845858;11428!GO:0016620;oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor;0.0414499359845858;28200!GO:0045333;cellular respiration;0.0414499359845858;11428!GO:0003729;mRNA binding;0.0414499359845858;11428!GO:0051187;cofactor catabolic process;0.0433320978832634;11428!GO:0006084;acetyl-CoA metabolic process;0.045140128544238;11428!GO:0008652;amino acid biosynthetic process;0.0455835397780651;13361!GO:0016903;oxidoreductase activity, acting on the aldehyde or oxo group of donors;0.0471976368569752;28200!GO:0044255;cellular lipid metabolic 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|gostat_on_MCL_coexpression=GO:0006720;isoprenoid metabolic process;0.00921864035950844;28200,17117!GO:0008111;alpha-methylacyl-CoA racemase activity;0.0107482502539566;17117!GO:0006545;glycine biosynthetic process;0.0107482502539566;13361!GO:0004371;glycerone kinase activity;0.0107482502539566;225913!GO:0004146;dihydrofolate reductase activity;0.0107482502539566;13361!GO:0008300;isoprenoid catabolic process;0.0107482502539566;17117!GO:0042579;microbody;0.0107482502539566;28200,17117!GO:0005777;peroxisome;0.0107482502539566;28200,17117!GO:0003994;aconitate hydratase activity;0.0135507654932865;11428!GO:0030350;iron-responsive element binding;0.0135507654932865;11428!GO:0050662;coenzyme binding;0.0135507654932865;226564,13361!GO:0004995;tachykinin receptor activity;0.0173476077320651;21336!GO:0016829;lyase activity;0.0182546376454438;11428,225913!GO:0001758;retinal dehydrogenase activity;0.0182546376454438;28200!GO:0004090;carbonyl reductase (NADPH) activity;0.0182546376454438;28200!GO:0048037;cofactor binding;0.0182546376454438;226564,13361!GO:0043288;apocarotenoid metabolic process;0.0182546376454438;28200!GO:0042574;retinal metabolic process;0.0182546376454438;28200!GO:0004499;flavin-containing monooxygenase activity;0.0182546376454438;226564!GO:0016491;oxidoreductase activity;0.0198160634969006;226564,13361,28200!GO:0009070;serine family amino acid biosynthetic process;0.0198160634969006;13361!GO:0006544;glycine metabolic process;0.0252121552214093;13361!GO:0050661;NADP binding;0.029694797603961;13361!GO:0016646;oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor;0.029694797603961;13361!GO:0016854;racemase and epimerase activity;0.029694797603961;17117!GO:0048265;response to pain;0.029694797603961;21336!GO:0016101;diterpenoid metabolic process;0.029694797603961;28200!GO:0001523;retinoid metabolic process;0.029694797603961;28200!GO:0006721;terpenoid metabolic process;0.0334383196327042;28200!GO:0006776;vitamin A metabolic process;0.0369292419083422;28200!GO:0009069;serine family amino acid metabolic process;0.0379653600349381;13361!GO:0051539;4 iron, 4 sulfur cluster binding;0.0395410453392476;11428!GO:0006071;glycerol metabolic process;0.0395410453392476;225913!GO:0019751;polyol metabolic process;0.0395410453392476;225913!GO:0016645;oxidoreductase activity, acting on the CH-NH group of donors;0.0395410453392476;13361!GO:0006775;fat-soluble vitamin metabolic process;0.0399409936252014;28200!GO:0016709;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen;0.0399409936252014;226564!GO:0006099;tricarboxylic acid cycle;0.0399409936252014;11428!GO:0055072;iron ion homeostasis;0.0399409936252014;11428!GO:0006879;cellular iron ion homeostasis;0.0399409936252014;11428!GO:0033555;multicellular organismal response to stress;0.0399409936252014;21336!GO:0046356;acetyl-CoA catabolic process;0.0399409936252014;11428!GO:0044248;cellular catabolic process;0.0399409936252014;11428,17117!GO:0006091;generation of precursor metabolites and energy;0.0399409936252014;226564,11428!GO:0009060;aerobic respiration;0.0399409936252014;11428!GO:0044242;cellular lipid catabolic process;0.0414499359845858;17117!GO:0009109;coenzyme catabolic process;0.0414499359845858;11428!GO:0016620;oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor;0.0414499359845858;28200!GO:0045333;cellular respiration;0.0414499359845858;11428!GO:0003729;mRNA binding;0.0414499359845858;11428!GO:0051187;cofactor catabolic process;0.0433320978832634;11428!GO:0006084;acetyl-CoA metabolic process;0.045140128544238;11428!GO:0008652;amino acid biosynthetic process;0.0455835397780651;13361!GO:0016903;oxidoreductase activity, acting on the aldehyde or oxo group of donors;0.0471976368569752;28200!GO:0044255;cellular lipid metabolic process;0.0471976368569752;28200,17117!GO:0042923;neuropeptide binding;0.0471976368569752;21336!GO:0008188;neuropeptide receptor activity;0.0471976368569752;21336!GO:0009056;catabolic process;0.0485941260019537;11428,17117!GO:0051536;iron-sulfur cluster binding;0.0485941260019537;11428!GO:0019748;secondary metabolic process;0.0485941260019537;28200!GO:0051540;metal cluster binding;0.0485941260019537;11428!
|ontology_enrichment_celltype=CL:0000066!8.90e-07!25
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000160!6.27e-15!31;UBERON:0005172!7.10e-14!49;UBERON:0005173!7.10e-14!49;UBERON:0002417!7.10e-14!49;UBERON:0000916!7.10e-14!49;UBERON:0009854!3.30e-13!23;UBERON:0009856!3.30e-13!23;UBERON:0002107!6.61e-13!22;UBERON:0007499!6.61e-13!22;UBERON:0006925!6.61e-13!22;UBERON:0009497!6.61e-13!22;UBERON:0000015!6.61e-13!22;UBERON:0002423!6.61e-13!22;UBERON:0006235!6.61e-13!22;UBERON:0008835!6.61e-13!22;UBERON:0003894!6.61e-13!22;UBERON:0004161!6.61e-13!22;UBERON:0008836!6.61e-13!22;UBERON:0005409!2.32e-12!47;UBERON:0002365!7.08e-11!25;UBERON:0002330!7.08e-11!25;UBERON:0005177!2.69e-10!79;UBERON:0003104!3.10e-10!61;UBERON:0009142!3.10e-10!61;UBERON:0000344!3.05e-09!15;UBERON:0009569!3.29e-09!66;UBERON:0003914!4.53e-09!47;UBERON:0005256!1.01e-08!45;UBERON:0002100!1.19e-08!90;UBERON:0001007!1.88e-08!116;UBERON:0001555!1.88e-08!116;UBERON:0007026!1.88e-08!116;UBERON:0001242!2.49e-08!13;UBERON:0000060!2.49e-08!13;UBERON:0001262!2.49e-08!13;UBERON:0004786!2.49e-08!13;UBERON:0004119!3.16e-08!118;UBERON:0000925!3.16e-08!118;UBERON:0006595!3.16e-08!118;UBERON:0004921!8.80e-08!114
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.433653,0.330161,0.394491,0.227651,0.40827,0.495658,0.448965,0.468136,0.0330111,0.453212,0.484001,0.146657,1.26558,0.24249,0,0.696644,0.22065,1.34367,0.247067,0.296085,1.55111,0.50668,0.226287,0.337218,0.534339,0.402559,0.428336,0.268347,0.319094,0.414842,0.796599,0.218674,0.364174,0.681042,0.0500417,1.78391,0.480503,0.559915,0.500908,0.224094,0.419787,0.371854,0.244285,0.158271,0.383899,1.49936,0.443479,0.133514,0.745859,0.679429,0.560572,0.633942,0.937018,0.954342,0.514504,0.764433,0.471658,0.770972,1.27615,0.776777,0.569793,0.952934,0.668331,0.525334,1.68713,1.08987,1.43807,0.772155,1.29123,0.840217,0.460931,1.14319,0.987652,0.371787,0.710896,0.364033,0.607043,0.759798,0.299972,0.463363,0.713779,0.568383,0.436063,0.873141,0.0800961,0.092683,0.319367,0.623015,1.60001,1.15927,0.878077,0.809272,0.232894,0.188213,0.515495,0.14449,0.812053,0.618454,0.278788,0.210602,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,0.439611,0.30446,0.297733,0.348012,0.921485,0.301014,1.15983,1.16629,0.633313,0.496288,0.398075,0.697928,0.207304,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.663857,0.90286,0.387557,1.05894,0.527782,1.18781,0.177062,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,0.956381,0.229209,1.10522,1.02444,0.938577,1.01208,1.3067,1.01974,0.561556,0.253271,0.352329,0.362302,1.1483,0.872292,0.763895,1.63697,0.669337,0.519673,0.602679,0.482466,3.08494
}}

Latest revision as of 15:56, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:93125094..93125131,+p2@Dhfr
Mm9::chr14:30823509..30823529,+p@chr14:30823509..30823529
+
Mm9::chr14:56097704..56097751,+p1@Dhrs4
Mm9::chr14:56097761..56097778,+p@chr14:56097761..56097778
+
Mm9::chr15:10911502..10911520,+p2@Amacr
Mm9::chr19:10678843..10678857,-p3@Dak
Mm9::chr1:164744073..164744084,-p1@Fmo4
Mm9::chr4:40090113..40090140,+p4@Aco1
Mm9::chr6:85087737..85087775,-p1@Spr


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:0006720isoprenoid metabolic process0.00921864035950844
GO:0008111alpha-methylacyl-CoA racemase activity0.0107482502539566
GO:0006545glycine biosynthetic process0.0107482502539566
GO:0004371glycerone kinase activity0.0107482502539566
GO:0004146dihydrofolate reductase activity0.0107482502539566
GO:0008300isoprenoid catabolic process0.0107482502539566
GO:0042579microbody0.0107482502539566
GO:0005777peroxisome0.0107482502539566
GO:0003994aconitate hydratase activity0.0135507654932865
GO:0030350iron-responsive element binding0.0135507654932865
GO:0050662coenzyme binding0.0135507654932865
GO:0004995tachykinin receptor activity0.0173476077320651
GO:0016829lyase activity0.0182546376454438
GO:0001758retinal dehydrogenase activity0.0182546376454438
GO:0004090carbonyl reductase (NADPH) activity0.0182546376454438
GO:0048037cofactor binding0.0182546376454438
GO:0043288apocarotenoid metabolic process0.0182546376454438
GO:0042574retinal metabolic process0.0182546376454438
GO:0004499flavin-containing monooxygenase activity0.0182546376454438
GO:0016491oxidoreductase activity0.0198160634969006
GO:0009070serine family amino acid biosynthetic process0.0198160634969006
GO:0006544glycine metabolic process0.0252121552214093
GO:0050661NADP binding0.029694797603961
GO:0016646oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor0.029694797603961
GO:0016854racemase and epimerase activity0.029694797603961
GO:0048265response to pain0.029694797603961
GO:0016101diterpenoid metabolic process0.029694797603961
GO:0001523retinoid metabolic process0.029694797603961
GO:0006721terpenoid metabolic process0.0334383196327042
GO:0006776vitamin A metabolic process0.0369292419083422
GO:0009069serine family amino acid metabolic process0.0379653600349381
GO:00515394 iron, 4 sulfur cluster binding0.0395410453392476
GO:0006071glycerol metabolic process0.0395410453392476
GO:0019751polyol metabolic process0.0395410453392476
GO:0016645oxidoreductase activity, acting on the CH-NH group of donors0.0395410453392476
GO:0006775fat-soluble vitamin metabolic process0.0399409936252014
GO:0016709oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NADH or NADPH as one donor, and incorporation of one atom of oxygen0.0399409936252014
GO:0006099tricarboxylic acid cycle0.0399409936252014
GO:0055072iron ion homeostasis0.0399409936252014
GO:0006879cellular iron ion homeostasis0.0399409936252014
GO:0033555multicellular organismal response to stress0.0399409936252014
GO:0046356acetyl-CoA catabolic process0.0399409936252014
GO:0044248cellular catabolic process0.0399409936252014
GO:0006091generation of precursor metabolites and energy0.0399409936252014
GO:0009060aerobic respiration0.0399409936252014
GO:0044242cellular lipid catabolic process0.0414499359845858
GO:0009109coenzyme catabolic process0.0414499359845858
GO:0016620oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor0.0414499359845858
GO:0045333cellular respiration0.0414499359845858
GO:0003729mRNA binding0.0414499359845858
GO:0051187cofactor catabolic process0.0433320978832634
GO:0006084acetyl-CoA metabolic process0.045140128544238
GO:0008652amino acid biosynthetic process0.0455835397780651
GO:0016903oxidoreductase activity, acting on the aldehyde or oxo group of donors0.0471976368569752
GO:0044255cellular lipid metabolic process0.0471976368569752
GO:0042923neuropeptide binding0.0471976368569752
GO:0008188neuropeptide receptor activity0.0471976368569752
GO:0009056catabolic process0.0485941260019537
GO:0051536iron-sulfur cluster binding0.0485941260019537
GO:0019748secondary metabolic process0.0485941260019537
GO:0051540metal cluster binding0.0485941260019537



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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
epithelial cell8.90e-0725

Uber Anatomy
Ontology termp-valuen
intestine6.27e-1531
abdomen element7.10e-1449
abdominal segment element7.10e-1449
abdominal segment of trunk7.10e-1449
abdomen7.10e-1449
digestive tract diverticulum3.30e-1323
sac3.30e-1323
liver6.61e-1322
epithelial sac6.61e-1322
digestive gland6.61e-1322
epithelium of foregut-midgut junction6.61e-1322
anatomical boundary6.61e-1322
hepatobiliary system6.61e-1322
foregut-midgut junction6.61e-1322
hepatic diverticulum6.61e-1322
liver primordium6.61e-1322
septum transversum6.61e-1322
liver bud6.61e-1322
gastrointestinal system2.32e-1247
exocrine gland7.08e-1125
exocrine system7.08e-1125
trunk region element2.69e-1079
mesenchyme3.10e-1061
entire embryonic mesenchyme3.10e-1061
mucosa3.05e-0915
subdivision of trunk3.29e-0966
epithelial tube4.53e-0947
trunk mesenchyme1.01e-0845
trunk1.19e-0890
digestive system1.88e-08116
digestive tract1.88e-08116
primitive gut1.88e-08116
intestinal mucosa2.49e-0813
anatomical wall2.49e-0813
wall of intestine2.49e-0813
gastrointestinal system mucosa2.49e-0813
endoderm-derived structure3.16e-08118
endoderm3.16e-08118
presumptive endoderm3.16e-08118
subdivision of digestive tract8.80e-08114


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
MA0014.10.119217
MA0017.10.726051
MA0019.10.642876
MA0024.13.05882
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
MA0048.10.993388
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.221677
MA0056.10
MA0057.10.258928
MA0058.10.305206
MA0059.10.316585
MA0060.10.169058
MA0061.10.194456
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.077274
MA0069.11.96621
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.10.00108891
MA0074.10.488775
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
MA0092.10.362847
MA0093.10.2553
MA0095.10
MA0098.10
MA0100.11.20151
MA0101.10.324888
MA0103.10.272167
MA0105.10.35523
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.11.68389
MA0115.10.921497
MA0116.10.238371
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
MA0139.10.867077
MA0140.10.477483
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.568165
MA0145.10.200183
MA0146.11.46813
MA0147.10.205697
MA0148.10.410398
MA0149.10.330018
MA0062.21.21132
MA0035.20.482026
MA0039.21.67243
MA0138.21.52535
MA0002.20.145685
MA0137.20.287486
MA0104.20.157347
MA0047.20.533516
MA0112.20.200175
MA0065.20.200864
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.0809407
MA0155.10.845235
MA0156.10.763978
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.10.348617
MA0163.10.0600297
MA0164.10.508398
MA0080.20.737531
MA0018.20.51781
MA0099.20.624421
MA0079.20.33524
MA0102.21.5442
MA0258.10.180934
MA0259.10.196451
MA0442.10
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