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MCL coexpression mm9:652: Difference between revisions

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{{MCL_coexpression_mm9
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794678253004593,0.94128070561822,0.0760168881589905,0.220572027003917,0.188495428553301|gostat_on_MCL_coexpression=GO:0006066;alcohol metabolic process;0.00410307789521319;18563,218865,19013!GO:0019752;carboxylic acid metabolic process;0.00410307789521319;18563,218865,19013!GO:0006082;organic acid metabolic process;0.00410307789521319;18563,218865,19013!GO:0008812;choline dehydrogenase activity;0.00410307789521319;218865!GO:0004736;pyruvate carboxylase activity;0.00410307789521319;18563!GO:0031455;glycine betaine metabolic process;0.00410307789521319;218865!GO:0006578;betaine biosynthetic process;0.00410307789521319;218865!GO:0031456;glycine betaine biosynthetic process;0.00410307789521319;218865!GO:0019285;glycine betaine biosynthetic process from choline;0.00410307789521319;218865!GO:0006577;betaine metabolic process;0.00410307789521319;218865!GO:0015362;high affinity sodium:dicarboxylate symporter activity;0.00410307789521319;114644!GO:0006006;glucose metabolic process;0.00410307789521319;18563,19013!GO:0019318;hexose metabolic process;0.0065005020284588;18563,19013!GO:0005996;monosaccharide metabolic process;0.0065005020284588;18563,19013!GO:0019695;choline metabolic process;0.0065005020284588;218865!GO:0042439;ethanolamine and derivative metabolic process;0.0114689602854353;218865!GO:0009374;biotin binding;0.0114689602854353;18563!GO:0032787;monocarboxylic acid metabolic process;0.013096251318891;18563,19013!GO:0005743;mitochondrial inner membrane;0.0142120590508497;18563,218865!GO:0019866;organelle inner membrane;0.0142120590508497;18563,218865!GO:0031966;mitochondrial membrane;0.0142120590508497;18563,218865!GO:0044262;cellular carbohydrate metabolic process;0.0142120590508497;18563,19013!GO:0019217;regulation of fatty acid metabolic process;0.0142120590508497;19013!GO:0016885;ligase activity, forming carbon-carbon bonds;0.0142120590508497;18563!GO:0005740;mitochondrial envelope;0.0148516707081126;18563,218865!GO:0017153;sodium:dicarboxylate symporter activity;0.0149912985343832;114644!GO:0006835;dicarboxylic acid transport;0.0173968011642717;114644!GO:0005310;dicarboxylic acid transmembrane transporter activity;0.0173968011642717;114644!GO:0044429;mitochondrial part;0.0177160223997982;18563,218865!GO:0005975;carbohydrate metabolic process;0.0205855343660068;18563,19013!GO:0031975;envelope;0.0224742366795592;18563,218865!GO:0031967;organelle envelope;0.0224742366795592;18563,218865!GO:0006094;gluconeogenesis;0.0250743263206327;18563!GO:0015296;anion:cation symporter activity;0.0256832636280242;114644!GO:0005343;organic acid:sodium symporter activity;0.0256832636280242;114644!GO:0019216;regulation of lipid metabolic process;0.0256832636280242;19013!GO:0006090;pyruvate metabolic process;0.0276135025934446;18563!GO:0019319;hexose biosynthetic process;0.0294410289118389;18563!GO:0042401;biogenic amine biosynthetic process;0.0296530734806422;218865!GO:0046165;alcohol biosynthetic process;0.0296530734806422;18563!GO:0046364;monosaccharide biosynthetic process;0.0296530734806422;18563!GO:0044255;cellular lipid metabolic process;0.030747846169631;18563,19013!GO:0042398;amino acid derivative biosynthetic process;0.0311821039025154;218865!GO:0031090;organelle membrane;0.0311821039025154;18563,218865!GO:0006629;lipid metabolic process;0.0376562959052965;18563,19013!GO:0015370;solute:sodium symporter activity;0.0422184080370688;114644!GO:0003707;steroid hormone receptor activity;0.0485086249414863;19013!GO:0004879;ligand-dependent nuclear receptor 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|gostat_on_MCL_coexpression=GO:0006066;alcohol metabolic process;0.00410307789521319;18563,218865,19013!GO:0019752;carboxylic acid metabolic process;0.00410307789521319;18563,218865,19013!GO:0006082;organic acid metabolic process;0.00410307789521319;18563,218865,19013!GO:0008812;choline dehydrogenase activity;0.00410307789521319;218865!GO:0004736;pyruvate carboxylase activity;0.00410307789521319;18563!GO:0031455;glycine betaine metabolic process;0.00410307789521319;218865!GO:0006578;betaine biosynthetic process;0.00410307789521319;218865!GO:0031456;glycine betaine biosynthetic process;0.00410307789521319;218865!GO:0019285;glycine betaine biosynthetic process from choline;0.00410307789521319;218865!GO:0006577;betaine metabolic process;0.00410307789521319;218865!GO:0015362;high affinity sodium:dicarboxylate symporter activity;0.00410307789521319;114644!GO:0006006;glucose metabolic process;0.00410307789521319;18563,19013!GO:0019318;hexose metabolic process;0.0065005020284588;18563,19013!GO:0005996;monosaccharide metabolic process;0.0065005020284588;18563,19013!GO:0019695;choline metabolic process;0.0065005020284588;218865!GO:0042439;ethanolamine and derivative metabolic process;0.0114689602854353;218865!GO:0009374;biotin binding;0.0114689602854353;18563!GO:0032787;monocarboxylic acid metabolic process;0.013096251318891;18563,19013!GO:0005743;mitochondrial inner membrane;0.0142120590508497;18563,218865!GO:0019866;organelle inner membrane;0.0142120590508497;18563,218865!GO:0031966;mitochondrial membrane;0.0142120590508497;18563,218865!GO:0044262;cellular carbohydrate metabolic process;0.0142120590508497;18563,19013!GO:0019217;regulation of fatty acid metabolic process;0.0142120590508497;19013!GO:0016885;ligase activity, forming carbon-carbon bonds;0.0142120590508497;18563!GO:0005740;mitochondrial envelope;0.0148516707081126;18563,218865!GO:0017153;sodium:dicarboxylate symporter activity;0.0149912985343832;114644!GO:0006835;dicarboxylic acid transport;0.0173968011642717;114644!GO:0005310;dicarboxylic acid transmembrane transporter activity;0.0173968011642717;114644!GO:0044429;mitochondrial part;0.0177160223997982;18563,218865!GO:0005975;carbohydrate metabolic process;0.0205855343660068;18563,19013!GO:0031975;envelope;0.0224742366795592;18563,218865!GO:0031967;organelle envelope;0.0224742366795592;18563,218865!GO:0006094;gluconeogenesis;0.0250743263206327;18563!GO:0015296;anion:cation symporter activity;0.0256832636280242;114644!GO:0005343;organic acid:sodium symporter activity;0.0256832636280242;114644!GO:0019216;regulation of lipid metabolic process;0.0256832636280242;19013!GO:0006090;pyruvate metabolic process;0.0276135025934446;18563!GO:0019319;hexose biosynthetic process;0.0294410289118389;18563!GO:0042401;biogenic amine biosynthetic process;0.0296530734806422;218865!GO:0046165;alcohol biosynthetic process;0.0296530734806422;18563!GO:0046364;monosaccharide biosynthetic process;0.0296530734806422;18563!GO:0044255;cellular lipid metabolic process;0.030747846169631;18563,19013!GO:0042398;amino acid derivative biosynthetic process;0.0311821039025154;218865!GO:0031090;organelle membrane;0.0311821039025154;18563,218865!GO:0006629;lipid metabolic process;0.0376562959052965;18563,19013!GO:0015370;solute:sodium symporter activity;0.0422184080370688;114644!GO:0003707;steroid hormone receptor activity;0.0485086249414863;19013!GO:0004879;ligand-dependent nuclear receptor activity;0.0485086249414863;19013!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005172!4.58e-19!49;UBERON:0005173!4.58e-19!49;UBERON:0002417!4.58e-19!49;UBERON:0000916!4.58e-19!49;UBERON:0002107!3.02e-17!22;UBERON:0007499!3.02e-17!22;UBERON:0006925!3.02e-17!22;UBERON:0009497!3.02e-17!22;UBERON:0000015!3.02e-17!22;UBERON:0002423!3.02e-17!22;UBERON:0006235!3.02e-17!22;UBERON:0008835!3.02e-17!22;UBERON:0003894!3.02e-17!22;UBERON:0004161!3.02e-17!22;UBERON:0008836!3.02e-17!22;UBERON:0009854!4.01e-16!23;UBERON:0009856!4.01e-16!23;UBERON:0002365!2.29e-15!25;UBERON:0002330!2.29e-15!25;UBERON:0009569!2.00e-13!66;UBERON:0003104!6.33e-12!61;UBERON:0009142!6.33e-12!61;UBERON:0005177!3.62e-10!79;UBERON:0005256!2.76e-09!45;UBERON:0002100!2.46e-07!90
|tfbs_overrepresentation_for_novel_motifs=0.29262,1.06312,0.269904,0.329881,0.176699,0.342839,0.425757,0.106126,0.112618,0.401738,0.385334,0.414631,0.106288,0.437133,1.05871,0,0.619876,0.170475,0.656134,1.06389,0.670854,0.521547,0.436294,0.520732,0.276437,0.4628,0.0908349,0.361771,0.213277,0.500344,0.349031,0.717576,0.168723,0.270473,0.19035,0.0246631,0.161521,0.411296,0.144953,0.123934,0.173534,0.353696,0.104243,0.191571,1.11259,0.319944,0.543674,0.376103,0.208261,0.215702,0.603113,0.488021,0.220536,0.855661,0.87275,0.443782,0.634658,0.40287,0.0851299,0.441884,0.698157,0.496904,0.120887,0.592318,0.45416,0.631188,1.00675,1.3527,1.65677,1.20659,0.253722,0.355763,0.126035,0.905636,0.277092,0.0742951,0.570456,0.532872,0.681539,0.242107,1.19172,0.636582,0.495545,0.682423,0.792744,0.00855221,0.143445,0.0651072,0.548334,1.51408,1.07554,0.797601,0.730003,0.181374,0.141946,0.129056,0.340672,0.732731,0.543917,0.0534645,0.943642,0.717305,0.838603,0.603683,0.602672,0.353298,0.660145,0.372438,0.246223,0.240055,0.286453,0.840348,1.26399,0.390066,1.0825,0.512539,0.337757,0.333247,0.621127,0.158673,0.910937,0.572279,0.464505,1.3176,1.13603,0.685116,0.433317,0.723425,1.00525,0.540802,0.821997,0.323373,0.976125,0.456508,1.10385,0.115066,0.300001,0.934673,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.354106,0.546641,1.84176,0.302077,0.178088,0.507931,0.0240729,0.857198,0.415832,0.455644,0.93735,0.488969,0.199652,0.790184,0.299755,1.06466,0.791909,0.685546,0.284483,0.593295,0.448733,0.160658,3.81216,2.37988
|tfbs_overrepresentation_jaspar=MA0003.1;0.570495,MA0004.1;0.330313,MA0006.1;0.186435,MA0007.1;0.316976,MA0009.1;1.75966,MA0014.1;0.44164,MA0017.1;1.76941,MA0019.1;0.567591,MA0024.1;0.70077,MA0025.1;0.971686,MA0027.1;2.37948,MA0028.1;0.194782,MA0029.1;0.679737,MA0030.1;0.686088,MA0031.1;0.651724,MA0038.1;0.462726,MA0040.1;0.755433,MA0041.1;0.263922,MA0042.1;0.252679,MA0043.1;0.837621,MA0046.1;1.83192,MA0048.1;0.440822,MA0050.1;0.95731,MA0051.1;0.471092,MA0052.1;0.76328,MA0055.1;1.79839,MA0056.1;0,MA0057.1;0.181039,MA0058.1;0.246908,MA0059.1;0.257372,MA0060.1;0.789184,MA0061.1;0.147394,MA0063.1;0,MA0066.1;0.452472,MA0067.1;1.08124,MA0068.1;0.187364,MA0069.1;0.76361,MA0070.1;0.75417,MA0071.1;0.955636,MA0072.1;0.745922,MA0073.1;0.0212456,MA0074.1;0.419185,MA0076.1;0.223625,MA0077.1;0.724865,MA0078.1;1.25398,MA0081.1;0.277253,MA0083.1;0.836845,MA0084.1;1.4063,MA0087.1;0.794721,MA0088.1;0.12124,MA0089.1;0,MA0090.1;0.299987,MA0091.1;0.342071,MA0092.1;0.300264,MA0093.1;0.58345,MA0095.1;0,MA0098.1;0,MA0100.1;0.408523,MA0101.1;0.265031,MA0103.1;0.216742,MA0105.1;0.0759118,MA0106.1;0.509454,MA0107.1;0.211681,MA0108.2;0.589413,MA0109.1;0,MA0111.1;0.312463,MA0113.1;0.482899,MA0114.1;2.0321,MA0115.1;0.84036,MA0116.1;1.04399,MA0117.1;0.808813,MA0119.1;0.733279,MA0122.1;0.828211,MA0124.1;1.02871,MA0125.1;0.955734,MA0130.1;0,MA0131.1;0.563262,MA0132.1;0,MA0133.1;0,MA0135.1;0.873285,MA0136.1;0.437601,MA0139.1;0.338099,MA0140.1;0.408417,MA0141.1;2.67467,MA0142.1;0.63775,MA0143.1;1.24578,MA0144.1;0.147954,MA0145.1;0.3137,MA0146.1;1.06665,MA0147.1;0.157258,MA0148.1;0.912216,MA0149.1;0.269772,MA0062.2;0.0791588,MA0035.2;0.412747,MA0039.2;0.0156442,MA0138.2;0.555696,MA0002.2;0.105469,MA0137.2;0.230686,MA0104.2;0.369356,MA0047.2;0.46201,MA0112.2;0.313687,MA0065.2;1.30208,MA0150.1;0.316876,MA0151.1;0,MA0152.1;0.46211,MA0153.1;2.06069,MA0154.1;0.195907,MA0155.1;0.0394399,MA0156.1;0.222905,MA0157.1;0.606944,MA0158.1;0,MA0159.1;0.165031,MA0160.1;0.347545,MA0161.1;0,MA0162.1;0.00661648,MA0163.1;0.820388,MA0164.1;0.437937,MA0080.2;0.212408,MA0018.2;0.446948,MA0099.2;0.549696,MA0079.2;0.150907,MA0102.2;1.45844,MA0258.1;1.34967,MA0259.1;0.455671,MA0442.1;0
}}

Latest revision as of 15:40, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:46512321..46512337,-p4@Timd2
Mm9::chr11:55031211..55031234,+p@chr11:55031211..55031234
+
Mm9::chr14:30822115..30822130,+p5@Chdh
Mm9::chr15:85602581..85602598,+p8@Ppara
Mm9::chr16:23029153..23029179,-p1@Kng2
Mm9::chr16:23029188..23029211,-p2@Kng2
Mm9::chr19:4594312..4594332,+p5@Pcx
Mm9::chr19:4594337..4594361,+p6@Pcx
Mm9::chr19:4594363..4594394,+p3@Pcx
Mm9::chr19:4594398..4594422,+p4@Pcx
Mm9::chr2:165298687..165298702,-p1@Slc13a3


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:0006066alcohol metabolic process0.00410307789521319
GO:0019752carboxylic acid metabolic process0.00410307789521319
GO:0006082organic acid metabolic process0.00410307789521319
GO:0008812choline dehydrogenase activity0.00410307789521319
GO:0004736pyruvate carboxylase activity0.00410307789521319
GO:0031455glycine betaine metabolic process0.00410307789521319
GO:0006578betaine biosynthetic process0.00410307789521319
GO:0031456glycine betaine biosynthetic process0.00410307789521319
GO:0019285glycine betaine biosynthetic process from choline0.00410307789521319
GO:0006577betaine metabolic process0.00410307789521319
GO:0015362high affinity sodium:dicarboxylate symporter activity0.00410307789521319
GO:0006006glucose metabolic process0.00410307789521319
GO:0019318hexose metabolic process0.0065005020284588
GO:0005996monosaccharide metabolic process0.0065005020284588
GO:0019695choline metabolic process0.0065005020284588
GO:0042439ethanolamine and derivative metabolic process0.0114689602854353
GO:0009374biotin binding0.0114689602854353
GO:0032787monocarboxylic acid metabolic process0.013096251318891
GO:0005743mitochondrial inner membrane0.0142120590508497
GO:0019866organelle inner membrane0.0142120590508497
GO:0031966mitochondrial membrane0.0142120590508497
GO:0044262cellular carbohydrate metabolic process0.0142120590508497
GO:0019217regulation of fatty acid metabolic process0.0142120590508497
GO:0016885ligase activity, forming carbon-carbon bonds0.0142120590508497
GO:0005740mitochondrial envelope0.0148516707081126
GO:0017153sodium:dicarboxylate symporter activity0.0149912985343832
GO:0006835dicarboxylic acid transport0.0173968011642717
GO:0005310dicarboxylic acid transmembrane transporter activity0.0173968011642717
GO:0044429mitochondrial part0.0177160223997982
GO:0005975carbohydrate metabolic process0.0205855343660068
GO:0031975envelope0.0224742366795592
GO:0031967organelle envelope0.0224742366795592
GO:0006094gluconeogenesis0.0250743263206327
GO:0015296anion:cation symporter activity0.0256832636280242
GO:0005343organic acid:sodium symporter activity0.0256832636280242
GO:0019216regulation of lipid metabolic process0.0256832636280242
GO:0006090pyruvate metabolic process0.0276135025934446
GO:0019319hexose biosynthetic process0.0294410289118389
GO:0042401biogenic amine biosynthetic process0.0296530734806422
GO:0046165alcohol biosynthetic process0.0296530734806422
GO:0046364monosaccharide biosynthetic process0.0296530734806422
GO:0044255cellular lipid metabolic process0.030747846169631
GO:0042398amino acid derivative biosynthetic process0.0311821039025154
GO:0031090organelle membrane0.0311821039025154
GO:0006629lipid metabolic process0.0376562959052965
GO:0015370solute:sodium symporter activity0.0422184080370688
GO:0003707steroid hormone receptor activity0.0485086249414863
GO:0004879ligand-dependent nuclear receptor activity0.0485086249414863



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
abdomen element4.58e-1949
abdominal segment element4.58e-1949
abdominal segment of trunk4.58e-1949
abdomen4.58e-1949
liver3.02e-1722
epithelial sac3.02e-1722
digestive gland3.02e-1722
epithelium of foregut-midgut junction3.02e-1722
anatomical boundary3.02e-1722
hepatobiliary system3.02e-1722
foregut-midgut junction3.02e-1722
hepatic diverticulum3.02e-1722
liver primordium3.02e-1722
septum transversum3.02e-1722
liver bud3.02e-1722
digestive tract diverticulum4.01e-1623
sac4.01e-1623
exocrine gland2.29e-1525
exocrine system2.29e-1525
subdivision of trunk2.00e-1366
mesenchyme6.33e-1261
entire embryonic mesenchyme6.33e-1261
trunk region element3.62e-1079
trunk mesenchyme2.76e-0945
trunk2.46e-0790


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)
MA0003.10.570495
MA0004.10.330313
MA0006.10.186435
MA0007.10.316976
MA0009.11.75966
MA0014.10.44164
MA0017.11.76941
MA0019.10.567591
MA0024.10.70077
MA0025.10.971686
MA0027.12.37948
MA0028.10.194782
MA0029.10.679737
MA0030.10.686088
MA0031.10.651724
MA0038.10.462726
MA0040.10.755433
MA0041.10.263922
MA0042.10.252679
MA0043.10.837621
MA0046.11.83192
MA0048.10.440822
MA0050.10.95731
MA0051.10.471092
MA0052.10.76328
MA0055.11.79839
MA0056.10
MA0057.10.181039
MA0058.10.246908
MA0059.10.257372
MA0060.10.789184
MA0061.10.147394
MA0063.10
MA0066.10.452472
MA0067.11.08124
MA0068.10.187364
MA0069.10.76361
MA0070.10.75417
MA0071.10.955636
MA0072.10.745922
MA0073.10.0212456
MA0074.10.419185
MA0076.10.223625
MA0077.10.724865
MA0078.11.25398
MA0081.10.277253
MA0083.10.836845
MA0084.11.4063
MA0087.10.794721
MA0088.10.12124
MA0089.10
MA0090.10.299987
MA0091.10.342071
MA0092.10.300264
MA0093.10.58345
MA0095.10
MA0098.10
MA0100.10.408523
MA0101.10.265031
MA0103.10.216742
MA0105.10.0759118
MA0106.10.509454
MA0107.10.211681
MA0108.20.589413
MA0109.10
MA0111.10.312463
MA0113.10.482899
MA0114.12.0321
MA0115.10.84036
MA0116.11.04399
MA0117.10.808813
MA0119.10.733279
MA0122.10.828211
MA0124.11.02871
MA0125.10.955734
MA0130.10
MA0131.10.563262
MA0132.10
MA0133.10
MA0135.10.873285
MA0136.10.437601
MA0139.10.338099
MA0140.10.408417
MA0141.12.67467
MA0142.10.63775
MA0143.11.24578
MA0144.10.147954
MA0145.10.3137
MA0146.11.06665
MA0147.10.157258
MA0148.10.912216
MA0149.10.269772
MA0062.20.0791588
MA0035.20.412747
MA0039.20.0156442
MA0138.20.555696
MA0002.20.105469
MA0137.20.230686
MA0104.20.369356
MA0047.20.46201
MA0112.20.313687
MA0065.21.30208
MA0150.10.316876
MA0151.10
MA0152.10.46211
MA0153.12.06069
MA0154.10.195907
MA0155.10.0394399
MA0156.10.222905
MA0157.10.606944
MA0158.10
MA0159.10.165031
MA0160.10.347545
MA0161.10
MA0162.10.00661648
MA0163.10.820388
MA0164.10.437937
MA0080.20.212408
MA0018.20.446948
MA0099.20.549696
MA0079.20.150907
MA0102.21.45844
MA0258.11.34967
MA0259.10.455671
MA0442.10
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