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MCL coexpression mm9:841: Difference between revisions

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{{MCL_coexpression_mm9
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dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity;0.00928461847680428;109264!GO:0004738;pyruvate dehydrogenase activity;0.00928461847680428;18597!GO:0008090;retrograde axon cargo transport;0.00928461847680428;13518!GO:0004739;pyruvate dehydrogenase (acetyl-transferring) activity;0.00928461847680428;18597!GO:0044262;cellular carbohydrate metabolic process;0.00928461847680428;109264,18597!GO:0031122;cytoplasmic microtubule organization and biogenesis;0.00928461847680428;13518!GO:0004470;malic enzyme activity;0.00928461847680428;109264!GO:0006108;malate metabolic process;0.0103156775094049;109264!GO:0005975;carbohydrate metabolic process;0.0104423344548168;109264,18597!GO:0016624;oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor;0.0104423344548168;18597!GO:0016615;malate dehydrogenase activity;0.0104423344548168;109264!GO:0009925;basal plasma membrane;0.0104423344548168;13518!GO:0060053;neurofilament 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|gostat_on_MCL_coexpression=GO:0030056;hemidesmosome;0.00928461847680428;13518!GO:0004473;malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity;0.00928461847680428;109264!GO:0004738;pyruvate dehydrogenase activity;0.00928461847680428;18597!GO:0008090;retrograde axon cargo transport;0.00928461847680428;13518!GO:0004739;pyruvate dehydrogenase (acetyl-transferring) activity;0.00928461847680428;18597!GO:0044262;cellular carbohydrate metabolic process;0.00928461847680428;109264,18597!GO:0031122;cytoplasmic microtubule organization and biogenesis;0.00928461847680428;13518!GO:0004470;malic enzyme activity;0.00928461847680428;109264!GO:0006108;malate metabolic process;0.0103156775094049;109264!GO:0005975;carbohydrate metabolic process;0.0104423344548168;109264,18597!GO:0016624;oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor;0.0104423344548168;18597!GO:0016615;malate dehydrogenase activity;0.0104423344548168;109264!GO:0009925;basal plasma membrane;0.0104423344548168;13518!GO:0060053;neurofilament cytoskeleton;0.0104423344548168;13518!GO:0045178;basal part of cell;0.0104423344548168;13518!GO:0043648;dicarboxylic acid metabolic process;0.0104423344548168;109264!GO:0008088;axon cargo transport;0.0109194899359178;13518!GO:0031110;regulation of microtubule polymerization or depolymerization;0.0134045032055733;13518!GO:0031109;microtubule polymerization or depolymerization;0.0136750999806115;13518!GO:0006100;tricarboxylic acid cycle intermediate metabolic process;0.0139185353958062;109264!GO:0051287;NAD binding;0.019434306341141;109264!GO:0044444;cytoplasmic part;0.0241329633513848;109264,18597,13518!GO:0016491;oxidoreductase activity;0.0246206447328127;109264,18597!GO:0030055;cell-matrix junction;0.0270341658124554;13518!GO:0016903;oxidoreductase activity, acting on the aldehyde or oxo group of donors;0.0281726907363467;18597!GO:0005739;mitochondrion;0.0293869201483859;109264,18597!GO:0006096;glycolysis;0.0293869201483859;18597!GO:0007050;cell cycle arrest;0.0293869201483859;13518!GO:0008017;microtubule binding;0.0293869201483859;13518!GO:0006007;glucose catabolic process;0.0296262072510759;18597!GO:0046365;monosaccharide catabolic process;0.0296262072510759;18597!GO:0019320;hexose catabolic process;0.0296262072510759;18597!GO:0051128;regulation of cellular component organization and biogenesis;0.0296262072510759;13518!GO:0015631;tubulin binding;0.0296262072510759;13518!GO:0046164;alcohol catabolic process;0.0296262072510759;18597!GO:0000226;microtubule cytoskeleton organization and biogenesis;0.0329035671846674;13518!GO:0044275;cellular carbohydrate catabolic process;0.0330111061329209;18597!GO:0016323;basolateral plasma membrane;0.0340829371096963;13518!GO:0016052;carbohydrate catabolic process;0.0341540971008432;18597!GO:0007018;microtubule-based movement;0.0383646209931261;13518!GO:0006006;glucose metabolic process;0.0431054408632943;18597!GO:0030705;cytoskeleton-dependent intracellular transport;0.0431054408632943;13518!GO:0016616;oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor;0.0472273373491732;109264!GO:0050662;coenzyme binding;0.0475000923347259;109264!GO:0045786;negative regulation of progression through cell cycle;0.0475000923347259;13518!GO:0016614;oxidoreductase activity, acting on CH-OH group of donors;0.0475000923347259;109264!GO:0045111;intermediate filament cytoskeleton;0.0475000923347259;13518!GO:0019318;hexose metabolic process;0.0499452758871698;18597!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004535!6.86e-08!23;UBERON:0001009!6.86e-08!23;UBERON:0007100!4.71e-07!18;UBERON:0000948!4.71e-07!18;UBERON:0005498!4.71e-07!18;UBERON:0004140!4.71e-07!18;UBERON:0009881!4.71e-07!18;UBERON:0004141!4.71e-07!18;UBERON:0003084!4.71e-07!18;UBERON:0007005!4.71e-07!18;UBERON:0004139!4.71e-07!18;UBERON:0004291!4.71e-07!18
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.706384,0.330161,1.02163,0.645379,1.05171,0.495658,0.146465,0.468136,0.0330111,0.453212,0.484001,0.88117,0.507558,1.9552,0,0.696644,0.22065,0.134657,0.528436,0.296085,0.179861,0.50668,0.226287,1.60644,0.534339,0.801525,0.428336,1.35822,0.319094,0.414842,0.796599,0.218674,0.113369,0.242923,0.281474,0.604998,0.480503,1.67947,0.167387,0.224094,0.419787,0.0422275,0.244285,0.317317,0.998423,0.618203,0.443479,0.314152,0.745859,0.679429,0.560572,0.30602,0.937018,0.954342,0.514504,0.279148,1.18878,0.12126,0.512521,0.776777,0.569793,0.163832,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.31262,0.151245,0.424998,0.987652,0.748687,0.107966,0.735293,0.607043,2.99702,0.299972,0.152219,0.713779,0.568383,0.14134,0.873141,0.395495,0.439624,0.319367,0.623015,1.60001,1.15927,0.878077,0.809272,0.657661,0.188213,0.17334,0.444003,1.90157,0.618454,0.278788,0.605162,0.796322,0.919715,0.680015,0.678976,1.07585,0.737915,0.439611,0.821842,0.297733,0.348012,0.921485,0.301014,0.458194,1.16629,0.222515,1.15833,0.398075,0.697928,0.207304,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.235546,0.90286,1.00644,1.05894,0.527782,1.18781,0.0467191,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,1.50578,1.92834,0.364791,0.229209,1.10522,0.659481,0.938577,1.01208,0.526881,1.01974,0.561556,0.253271,0.352329,0.362302,1.1483,3.34905,0.763895,0.345891,2.71035,0.519673,0.602679,0.482466,0.0435162
}}

Latest revision as of 15:58, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr1:34178286..34178303,+p11@Dst
Mm9::chr1:34178314..34178329,+p7@Dst
Mm9::chr5:122068874..122068934,-p1@Acad12
Mm9::chr6:86466214..86466234,-p1@uc009csb.1
Mm9::chr6:86466248..86466270,-p3@uc009csb.1
Mm9::chr6:86466277..86466290,-p4@uc009csb.1
Mm9::chr7:96781385..96781422,+p2@Me3
Mm9::chr7:96781461..96781503,+p5@Me3
Mm9::chrX:156576281..156576303,-p1@Pdha1


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:0030056hemidesmosome0.00928461847680428
GO:0004473malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) activity0.00928461847680428
GO:0004738pyruvate dehydrogenase activity0.00928461847680428
GO:0008090retrograde axon cargo transport0.00928461847680428
GO:0004739pyruvate dehydrogenase (acetyl-transferring) activity0.00928461847680428
GO:0044262cellular carbohydrate metabolic process0.00928461847680428
GO:0031122cytoplasmic microtubule organization and biogenesis0.00928461847680428
GO:0004470malic enzyme activity0.00928461847680428
GO:0006108malate metabolic process0.0103156775094049
GO:0005975carbohydrate metabolic process0.0104423344548168
GO:0016624oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor0.0104423344548168
GO:0016615malate dehydrogenase activity0.0104423344548168
GO:0009925basal plasma membrane0.0104423344548168
GO:0060053neurofilament cytoskeleton0.0104423344548168
GO:0045178basal part of cell0.0104423344548168
GO:0043648dicarboxylic acid metabolic process0.0104423344548168
GO:0008088axon cargo transport0.0109194899359178
GO:0031110regulation of microtubule polymerization or depolymerization0.0134045032055733
GO:0031109microtubule polymerization or depolymerization0.0136750999806115
GO:0006100tricarboxylic acid cycle intermediate metabolic process0.0139185353958062
GO:0051287NAD binding0.019434306341141
GO:0044444cytoplasmic part0.0241329633513848
GO:0016491oxidoreductase activity0.0246206447328127
GO:0030055cell-matrix junction0.0270341658124554
GO:0016903oxidoreductase activity, acting on the aldehyde or oxo group of donors0.0281726907363467
GO:0005739mitochondrion0.0293869201483859
GO:0006096glycolysis0.0293869201483859
GO:0007050cell cycle arrest0.0293869201483859
GO:0008017microtubule binding0.0293869201483859
GO:0006007glucose catabolic process0.0296262072510759
GO:0046365monosaccharide catabolic process0.0296262072510759
GO:0019320hexose catabolic process0.0296262072510759
GO:0051128regulation of cellular component organization and biogenesis0.0296262072510759
GO:0015631tubulin binding0.0296262072510759
GO:0046164alcohol catabolic process0.0296262072510759
GO:0000226microtubule cytoskeleton organization and biogenesis0.0329035671846674
GO:0044275cellular carbohydrate catabolic process0.0330111061329209
GO:0016323basolateral plasma membrane0.0340829371096963
GO:0016052carbohydrate catabolic process0.0341540971008432
GO:0007018microtubule-based movement0.0383646209931261
GO:0006006glucose metabolic process0.0431054408632943
GO:0030705cytoskeleton-dependent intracellular transport0.0431054408632943
GO:0016616oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor0.0472273373491732
GO:0050662coenzyme binding0.0475000923347259
GO:0045786negative regulation of progression through cell cycle0.0475000923347259
GO:0016614oxidoreductase activity, acting on CH-OH group of donors0.0475000923347259
GO:0045111intermediate filament cytoskeleton0.0475000923347259
GO:0019318hexose metabolic process0.0499452758871698



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
cardiovascular system6.86e-0823
circulatory system6.86e-0823
primary circulatory organ4.71e-0718
heart4.71e-0718
primitive heart tube4.71e-0718
primary heart field4.71e-0718
anterior lateral plate mesoderm4.71e-0718
heart tube4.71e-0718
heart primordium4.71e-0718
cardiac mesoderm4.71e-0718
cardiogenic plate4.71e-0718
heart rudiment4.71e-0718


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
MA0006.10.670874
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
MA0048.10.0824771
MA0050.11.10321
MA0051.11.34084
MA0052.10.84317
MA0055.11.02213
MA0056.10
MA0057.10.549903
MA0058.10.305206
MA0059.10.849123
MA0060.10.169058
MA0061.10.194456
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.077274
MA0069.10.843506
MA0070.13.22936
MA0071.11.93072
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
MA0088.10.18495
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.362847
MA0093.10.2553
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.324888
MA0103.10.748482
MA0105.10.35523
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.11.36684
MA0114.10.19245
MA0115.10.921497
MA0116.10.238371
MA0117.10.88947
MA0119.11.56471
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.143341
MA0140.10.477483
MA0141.13.05378
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.10.0543321
MA0146.10.0111657
MA0147.10.593505
MA0148.12.78137
MA0149.10.330018
MA0062.20.365726
MA0035.20.482026
MA0039.20.0946163
MA0138.22.58639
MA0002.20.877049
MA0137.20.287486
MA0104.20.926067
MA0047.22.27139
MA0112.20.442124
MA0065.20.44341
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.0809407
MA0155.10.0631765
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.11.15501
MA0160.12.79475
MA0161.10
MA0162.10.0143037
MA0163.10.321031
MA0164.10.508398
MA0080.20.267388
MA0018.20.51781
MA0099.20.624421
MA0079.20.0880689
MA0102.21.5442
MA0258.10.180934
MA0259.10.196451
MA0442.10
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