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MCL coexpression mm9:767: Difference between revisions

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{{MCL_coexpression_mm9
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reductase activity;0.00803520882412023;110391!GO:0046874;quinolinate metabolic process;0.00803520882412023;266645!GO:0001760;aminocarboxymuconate-semialdehyde decarboxylase activity;0.00803520882412023;266645!GO:0046146;tetrahydrobiopterin metabolic process;0.0284510300394729;110391!GO:0006729;tetrahydrobiopterin biosynthetic process;0.0284510300394729;110391!GO:0005776;autophagic vacuole;0.0284510300394729;57436!GO:0043648;dicarboxylic acid metabolic process;0.0284510300394729;266645!GO:0016646;oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor;0.0284510300394729;110391!GO:0042559;pteridine and derivative biosynthetic process;0.0284510300394729;110391!GO:0019438;aromatic compound biosynthetic process;0.0284510300394729;110391!GO:0042558;pteridine and derivative metabolic process;0.0284510300394729;110391!GO:0016645;oxidoreductase activity, acting on the CH-NH group of donors;0.0400924815146338;110391!GO:0016831;carboxy-lyase 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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.202843190349958,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.789759981102069,0.372901452322848,0.873694753587128,0.744170496539592,0.701761516724823,0.472203634371576,0,0,0,0,0,0,0,0,0,0,0.500989894871126,0,0,0,0,0,0,0.0482820047261801,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.137524551899174,0.308698813725989,0.340901754499126,0.461962903546588,0.952838338859265,1.01127115272661,1.02632807159994,0.598191300042536,0,0,0,0,0,0,0,0.172137356316638,0.260949644910126,0,0.241616673082865,0.28693070537148,0.400619706372722,0.798748063580569,1.28629596697422,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.034489466458534,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.051739095208956,0,0,0.098117166361508,0,0.0388749848471105,0,0,0,0,0,0,0,0.128033729919821,0,0,0,0,0,0.0372877311781236,0,0,0,0,0,0,0.0191122501385941,0,0,0,0.146356659973704,0,0,0
|gostat_on_MCL_coexpression=GO:0004155;6,7-dihydropteridine reductase activity;0.00803520882412023;110391!GO:0046874;quinolinate metabolic process;0.00803520882412023;266645!GO:0001760;aminocarboxymuconate-semialdehyde decarboxylase activity;0.00803520882412023;266645!GO:0046146;tetrahydrobiopterin metabolic process;0.0284510300394729;110391!GO:0006729;tetrahydrobiopterin biosynthetic process;0.0284510300394729;110391!GO:0005776;autophagic vacuole;0.0284510300394729;57436!GO:0043648;dicarboxylic acid metabolic process;0.0284510300394729;266645!GO:0016646;oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor;0.0284510300394729;110391!GO:0042559;pteridine and derivative biosynthetic process;0.0284510300394729;110391!GO:0019438;aromatic compound biosynthetic process;0.0284510300394729;110391!GO:0042558;pteridine and derivative metabolic process;0.0284510300394729;110391!GO:0016645;oxidoreductase activity, acting on the CH-NH group of donors;0.0400924815146338;110391!GO:0016831;carboxy-lyase activity;0.0480793553574479;266645!
|ontology_enrichment_celltype=CL:0000181!5.18e-10!5;CL:0000417!5.18e-10!5;CL:0000668!5.18e-10!5;CL:0000412!5.18e-10!5;CL:0000182!5.18e-10!5
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005172!2.32e-22!49;UBERON:0005173!2.32e-22!49;UBERON:0002417!2.32e-22!49;UBERON:0000916!2.32e-22!49;UBERON:0002107!2.53e-20!22;UBERON:0007499!2.53e-20!22;UBERON:0006925!2.53e-20!22;UBERON:0009497!2.53e-20!22;UBERON:0000015!2.53e-20!22;UBERON:0002423!2.53e-20!22;UBERON:0006235!2.53e-20!22;UBERON:0008835!2.53e-20!22;UBERON:0003894!2.53e-20!22;UBERON:0004161!2.53e-20!22;UBERON:0008836!2.53e-20!22;UBERON:0009854!2.56e-19!23;UBERON:0009856!2.56e-19!23;UBERON:0002365!1.51e-17!25;UBERON:0002330!1.51e-17!25;UBERON:0003104!4.73e-17!61;UBERON:0009142!4.73e-17!61;UBERON:0009569!2.08e-15!66;UBERON:0005177!4.10e-12!79;UBERON:0002100!4.52e-10!90;UBERON:0005256!6.39e-10!45;UBERON:0002113!1.24e-09!14;UBERON:0003918!1.24e-09!14;UBERON:0011143!1.24e-09!14;UBERON:0005095!1.24e-09!14;UBERON:0007687!1.24e-09!14;UBERON:0003914!4.84e-08!47;UBERON:0006554!2.89e-07!18;UBERON:0001008!7.89e-07!19
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.0909519,0.330161,1.02163,0.227651,0.40827,0.495658,0.146465,0.154135,0.314043,0.453212,0.484001,0.146657,0.507558,0.680035,0,0.696644,0.62892,1.34367,0.247067,0.296085,0.403891,0.50668,0.64218,0.895255,1.32254,0.128175,0.428336,0.268347,0.656973,0.414842,0.796599,1.17111,0.113369,0.242923,0.137663,0.210533,0.480503,1.06548,0.167387,0.224094,0.419787,0.163087,1.2686,0.317317,0.383899,0.618203,0.443479,0.133514,0.271021,0.679429,0.560572,0.30602,0.937018,0.954342,0.514504,0.279148,0.471658,0.770972,0.512521,0.776777,0.569793,0.492158,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.31262,0.460931,0.0512949,0.987652,0.116281,0.107966,0.364033,0.607043,0.759798,0.299972,0.463363,0.713779,0.568383,0.436063,0.873141,0.0800961,1.88733,0.0965007,0.623015,1.60001,1.15927,0.878077,0.809272,0.232894,0.188213,0.515495,0.444003,0.812053,0.618454,0.0816605,0.210602,0.796322,0.919715,0.680015,6.7183,0.419366,0.737915,1.11973,0.30446,0.297733,0.348012,0.921485,0.814064,0.458194,1.16629,0.633313,0.0259088,0.398075,0.697928,0.207304,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,0.235546,0.90286,0.387557,1.05894,0.527782,1.18781,0.0467191,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,0.364791,0.229209,0.098204,0.041769,0.938577,0.178329,0.526881,1.01974,0.561556,0.705025,0.352329,0.362302,1.1483,0.872292,0.763895,1.63697,0.669337,0.519673,0.209556,0.482466,0.976805
}}

Latest revision as of 15:51, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:68614144..68614154,+p18@Rhobtb1
Mm9::chr13:54169098..54169109,+p@chr13:54169098..54169109
+
Mm9::chr1:129625982..129625995,+p1@Acmsd
Mm9::chr1:129626007..129626012,+p2@Acmsd
Mm9::chr5:45835830..45835845,-p4@Qdpr
Mm9::chr6:129483226..129483267,+p1@Gabarapl1
Mm9::chr6:129483269..129483286,+p5@Gabarapl1
Mm9::chr7:59143316..59143330,+p@chr7:59143316..59143330
+
Mm9::chr9:21796534..21796550,-p@chr9:21796534..21796550
-


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:00041556,7-dihydropteridine reductase activity0.00803520882412023
GO:0046874quinolinate metabolic process0.00803520882412023
GO:0001760aminocarboxymuconate-semialdehyde decarboxylase activity0.00803520882412023
GO:0046146tetrahydrobiopterin metabolic process0.0284510300394729
GO:0006729tetrahydrobiopterin biosynthetic process0.0284510300394729
GO:0005776autophagic vacuole0.0284510300394729
GO:0043648dicarboxylic acid metabolic process0.0284510300394729
GO:0016646oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor0.0284510300394729
GO:0042559pteridine and derivative biosynthetic process0.0284510300394729
GO:0019438aromatic compound biosynthetic process0.0284510300394729
GO:0042558pteridine and derivative metabolic process0.0284510300394729
GO:0016645oxidoreductase activity, acting on the CH-NH group of donors0.0400924815146338
GO:0016831carboxy-lyase activity0.0480793553574479



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
metabolising cell5.18e-105
endopolyploid cell5.18e-105
parenchymal cell5.18e-105
polyploid cell5.18e-105
hepatocyte5.18e-105

Uber Anatomy
Ontology termp-valuen
abdomen element2.32e-2249
abdominal segment element2.32e-2249
abdominal segment of trunk2.32e-2249
abdomen2.32e-2249
liver2.53e-2022
epithelial sac2.53e-2022
digestive gland2.53e-2022
epithelium of foregut-midgut junction2.53e-2022
anatomical boundary2.53e-2022
hepatobiliary system2.53e-2022
foregut-midgut junction2.53e-2022
hepatic diverticulum2.53e-2022
liver primordium2.53e-2022
septum transversum2.53e-2022
liver bud2.53e-2022
digestive tract diverticulum2.56e-1923
sac2.56e-1923
exocrine gland1.51e-1725
exocrine system1.51e-1725
mesenchyme4.73e-1761
entire embryonic mesenchyme4.73e-1761
subdivision of trunk2.08e-1566
trunk region element4.10e-1279
trunk4.52e-1090
trunk mesenchyme6.39e-1045
kidney1.24e-0914
kidney mesenchyme1.24e-0914
upper urinary tract1.24e-0914
kidney rudiment1.24e-0914
kidney field1.24e-0914
epithelial tube4.84e-0847
urinary system structure2.89e-0718
renal system7.89e-0719


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)
MA0003.10.170768
MA0004.11.02263
MA0006.10.670874
MA0007.10.38073
MA0009.10.82278
MA0014.10.119217
MA0017.10.726051
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
MA0041.10.865043
MA0042.10.837668
MA0043.10.918718
MA0046.11.99676
MA0048.10.0824771
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.0882028
MA0056.10
MA0057.10.0745664
MA0058.10.305206
MA0059.10.316585
MA0060.10.169058
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
MA0073.10.831547
MA0074.10.488775
MA0076.10.279739
MA0077.10.804033
MA0078.10.575205
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.10.0492918
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.362847
MA0093.10.709711
MA0095.10
MA0098.10
MA0100.11.20151
MA0101.10.324888
MA0103.10.272167
MA0105.10.109964
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.561811
MA0115.10.921497
MA0116.10.238371
MA0117.10.88947
MA0119.13.27824
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
MA0146.10.148686
MA0147.10.205697
MA0148.11.86014
MA0149.10.330018
MA0062.20.113962
MA0035.20.482026
MA0039.20.175249
MA0138.20.630612
MA0002.20.447007
MA0137.20.287486
MA0104.20.476119
MA0047.20.533516
MA0112.20.0543294
MA0065.20.44341
MA0150.10.991233
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.0809407
MA0155.10.226288
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.11.06259
MA0161.10
MA0162.10.582797
MA0163.10.321031
MA0164.11.26737
MA0080.20.267388
MA0018.20.51781
MA0099.20.624421
MA0079.20.13055
MA0102.21.5442
MA0258.10.180934
MA0259.10.196451
MA0442.10
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