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MCL coexpression mm9:3474: Difference between revisions

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{{MCL_coexpression_mm9
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element binding;0.00964198644664237;11428!GO:0003994;aconitate hydratase activity;0.00964198644664237;11428!GO:0006091;generation of precursor metabolites and energy;0.0146926514014748;11428,102632!GO:0003995;acyl-CoA dehydrogenase activity;0.0218360101574241;102632!GO:0051539;4 iron, 4 sulfur cluster binding;0.0218360101574241;11428!GO:0055072;iron ion homeostasis;0.0218360101574241;11428!GO:0006099;tricarboxylic acid cycle;0.0218360101574241;11428!GO:0006879;cellular iron ion homeostasis;0.0218360101574241;11428!GO:0046356;acetyl-CoA catabolic process;0.0218360101574241;11428!GO:0009060;aerobic respiration;0.0218360101574241;11428!GO:0009109;coenzyme catabolic process;0.0218360101574241;11428!GO:0045333;cellular respiration;0.0218360101574241;11428!GO:0003729;mRNA binding;0.0218360101574241;11428!GO:0051187;cofactor catabolic process;0.0218360101574241;11428!GO:0006084;acetyl-CoA metabolic process;0.0218360101574241;11428!GO:0016627;oxidoreductase activity, acting on the CH-CH group of donors;0.0230077630181863;102632!GO:0051536;iron-sulfur cluster binding;0.0230077630181863;11428!GO:0051540;metal cluster binding;0.0230077630181863;11428!GO:0016836;hydro-lyase activity;0.0248341587454829;11428!GO:0050660;FAD binding;0.0270470899900274;102632!GO:0016835;carbon-oxygen lyase activity;0.0270470899900274;11428!GO:0015980;energy derivation by oxidation of organic compounds;0.0288752440179602;11428!GO:0042579;microbody;0.0352706574318195;102632!GO:0005777;peroxisome;0.0352706574318195;102632!GO:0030005;cellular di-, tri-valent inorganic cation homeostasis;0.0362472931151761;11428!GO:0055066;di-, tri-valent inorganic cation homeostasis;0.0362472931151761;11428!GO:0030003;cellular cation homeostasis;0.0367401753938845;11428!GO:0055080;cation homeostasis;0.0367401753938845;11428!GO:0050662;coenzyme binding;0.0384474968968982;102632!GO:0006417;regulation of translation;0.0419545494583387;11428!GO:0031326;regulation of cellular biosynthetic 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|gostat_on_MCL_coexpression=GO:0030350;iron-responsive element binding;0.00964198644664237;11428!GO:0003994;aconitate hydratase activity;0.00964198644664237;11428!GO:0006091;generation of precursor metabolites and energy;0.0146926514014748;11428,102632!GO:0003995;acyl-CoA dehydrogenase activity;0.0218360101574241;102632!GO:0051539;4 iron, 4 sulfur cluster binding;0.0218360101574241;11428!GO:0055072;iron ion homeostasis;0.0218360101574241;11428!GO:0006099;tricarboxylic acid cycle;0.0218360101574241;11428!GO:0006879;cellular iron ion homeostasis;0.0218360101574241;11428!GO:0046356;acetyl-CoA catabolic process;0.0218360101574241;11428!GO:0009060;aerobic respiration;0.0218360101574241;11428!GO:0009109;coenzyme catabolic process;0.0218360101574241;11428!GO:0045333;cellular respiration;0.0218360101574241;11428!GO:0003729;mRNA binding;0.0218360101574241;11428!GO:0051187;cofactor catabolic process;0.0218360101574241;11428!GO:0006084;acetyl-CoA metabolic process;0.0218360101574241;11428!GO:0016627;oxidoreductase activity, acting on the CH-CH group of donors;0.0230077630181863;102632!GO:0051536;iron-sulfur cluster binding;0.0230077630181863;11428!GO:0051540;metal cluster binding;0.0230077630181863;11428!GO:0016836;hydro-lyase activity;0.0248341587454829;11428!GO:0050660;FAD binding;0.0270470899900274;102632!GO:0016835;carbon-oxygen lyase activity;0.0270470899900274;11428!GO:0015980;energy derivation by oxidation of organic compounds;0.0288752440179602;11428!GO:0042579;microbody;0.0352706574318195;102632!GO:0005777;peroxisome;0.0352706574318195;102632!GO:0030005;cellular di-, tri-valent inorganic cation homeostasis;0.0362472931151761;11428!GO:0055066;di-, tri-valent inorganic cation homeostasis;0.0362472931151761;11428!GO:0030003;cellular cation homeostasis;0.0367401753938845;11428!GO:0055080;cation homeostasis;0.0367401753938845;11428!GO:0050662;coenzyme binding;0.0384474968968982;102632!GO:0006417;regulation of translation;0.0419545494583387;11428!GO:0031326;regulation of cellular biosynthetic process;0.0424022794648206;11428!GO:0055082;cellular chemical homeostasis;0.0424022794648206;11428!GO:0006873;cellular ion homeostasis;0.0424022794648206;11428!GO:0016829;lyase activity;0.0424022794648206;11428!GO:0009889;regulation of biosynthetic process;0.0424022794648206;11428!GO:0006732;coenzyme metabolic process;0.0424022794648206;11428!GO:0050801;ion homeostasis;0.0424338769084272;11428!GO:0048037;cofactor binding;0.0424338769084272;102632!GO:0051186;cofactor metabolic process;0.0459977810919878;11428!GO:0048878;chemical homeostasis;0.0493368470455996;11428!GO:0019725;cellular homeostasis;0.0493368470455996;11428!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002365!2.26e-10!25;UBERON:0002330!2.26e-10!25;UBERON:0000160!2.45e-10!31;UBERON:0005177!1.06e-09!79;UBERON:0009854!2.09e-09!23;UBERON:0009856!2.09e-09!23;UBERON:0002107!5.86e-09!22;UBERON:0007499!5.86e-09!22;UBERON:0006925!5.86e-09!22;UBERON:0009497!5.86e-09!22;UBERON:0000015!5.86e-09!22;UBERON:0002423!5.86e-09!22;UBERON:0006235!5.86e-09!22;UBERON:0008835!5.86e-09!22;UBERON:0003894!5.86e-09!22;UBERON:0004161!5.86e-09!22;UBERON:0008836!5.86e-09!22;UBERON:0009569!1.12e-08!66;UBERON:0005172!1.29e-08!49;UBERON:0005173!1.29e-08!49;UBERON:0002417!1.29e-08!49;UBERON:0000916!1.29e-08!49;UBERON:0004119!1.46e-08!118;UBERON:0000925!1.46e-08!118;UBERON:0006595!1.46e-08!118;UBERON:0001007!1.85e-08!116;UBERON:0001555!1.85e-08!116;UBERON:0007026!1.85e-08!116;UBERON:0002100!1.94e-08!90;UBERON:0005409!2.60e-08!47;UBERON:0004921!8.90e-08!114;UBERON:0003104!1.49e-07!61;UBERON:0009142!1.49e-07!61;UBERON:0003914!2.10e-07!47;UBERON:0005256!3.58e-07!45
|tfbs_overrepresentation_for_novel_motifs=0.752782,0.193418,1.71649,0.801166,0.587814,0.81763,0.919454,0.467321,0.479531,0.66329,0.870507,0.906098,0.467629,0.933025,0.608226,0,1.14208,0.578045,0.448066,0.328717,0.679146,0.756749,0.932027,0.585919,0.731217,0.963352,0.437236,0.841386,0.64294,0.380786,0.825437,1.24901,0.575271,0.411696,0.608816,0.144706,0.563758,0.902078,0.536514,0.50014,0.582863,1.94114,0.261619,0.610669,0.922882,1.85291,1.05665,0.859154,0.235354,1.55852,1.12346,0.99279,0.371606,1.3966,1.41464,0.940919,0.657156,0.891887,0.425455,0.938668,1.22795,1.00308,1.23806,1.11142,0.953187,1.15459,1.55483,1.90983,1.22303,1.7608,0.700291,0.474956,0.284975,1.44925,0.416814,0.402065,0.411601,1.04436,1.20986,0.684144,0.476502,1.16055,1.00151,0.459035,1.32978,0.535545,0.195254,0.380977,1.06194,2.07346,1.62608,1.33496,1.26245,0.595071,0.531443,0.509215,0.464141,1.26539,1.05692,0.352122,0.563856,1.24872,1.37854,1.12409,1.12297,0.830796,1.18646,0.854628,0.689894,0.681267,0.744607,1.38039,0.685481,0.876299,1.63327,0.580657,1.1471,0.805461,1.14346,0.559153,1.45481,1.08896,0.965352,1.04338,1.68841,1.21376,0.928483,1.25534,1.55328,0.598722,1.36093,0.792832,1.52297,0.955954,1.65529,0.273451,0.762499,0.832891,1.60513,2.44352,2.04137,1.55966,0.978551,1.26,1.11604,0.831808,1.06002,2.40374,0.765221,0.589976,1.77018,0.260379,1.39822,0.516739,0.954936,1.48249,0.993889,0.622823,0.749933,1.79877,1.61484,1.32889,4.40049,0.741984,1.11251,0.94678,0.562367,2.09085,0.833542
}}

Latest revision as of 20:10, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr4:40090493..40090535,+p2@Aco1
Mm9::chr4:40090543..40090554,+p3@Aco1
Mm9::chr9:103966008..103966040,+p2@Acad11


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:0030350iron-responsive element binding0.00964198644664237
GO:0003994aconitate hydratase activity0.00964198644664237
GO:0006091generation of precursor metabolites and energy0.0146926514014748
GO:0003995acyl-CoA dehydrogenase activity0.0218360101574241
GO:00515394 iron, 4 sulfur cluster binding0.0218360101574241
GO:0055072iron ion homeostasis0.0218360101574241
GO:0006099tricarboxylic acid cycle0.0218360101574241
GO:0006879cellular iron ion homeostasis0.0218360101574241
GO:0046356acetyl-CoA catabolic process0.0218360101574241
GO:0009060aerobic respiration0.0218360101574241
GO:0009109coenzyme catabolic process0.0218360101574241
GO:0045333cellular respiration0.0218360101574241
GO:0003729mRNA binding0.0218360101574241
GO:0051187cofactor catabolic process0.0218360101574241
GO:0006084acetyl-CoA metabolic process0.0218360101574241
GO:0016627oxidoreductase activity, acting on the CH-CH group of donors0.0230077630181863
GO:0051536iron-sulfur cluster binding0.0230077630181863
GO:0051540metal cluster binding0.0230077630181863
GO:0016836hydro-lyase activity0.0248341587454829
GO:0050660FAD binding0.0270470899900274
GO:0016835carbon-oxygen lyase activity0.0270470899900274
GO:0015980energy derivation by oxidation of organic compounds0.0288752440179602
GO:0042579microbody0.0352706574318195
GO:0005777peroxisome0.0352706574318195
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0362472931151761
GO:0055066di-, tri-valent inorganic cation homeostasis0.0362472931151761
GO:0030003cellular cation homeostasis0.0367401753938845
GO:0055080cation homeostasis0.0367401753938845
GO:0050662coenzyme binding0.0384474968968982
GO:0006417regulation of translation0.0419545494583387
GO:0031326regulation of cellular biosynthetic process0.0424022794648206
GO:0055082cellular chemical homeostasis0.0424022794648206
GO:0006873cellular ion homeostasis0.0424022794648206
GO:0016829lyase activity0.0424022794648206
GO:0009889regulation of biosynthetic process0.0424022794648206
GO:0006732coenzyme metabolic process0.0424022794648206
GO:0050801ion homeostasis0.0424338769084272
GO:0048037cofactor binding0.0424338769084272
GO:0051186cofactor metabolic process0.0459977810919878
GO:0048878chemical homeostasis0.0493368470455996
GO:0019725cellular homeostasis0.0493368470455996



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
exocrine gland2.26e-1025
exocrine system2.26e-1025
intestine2.45e-1031
trunk region element1.06e-0979
digestive tract diverticulum2.09e-0923
sac2.09e-0923
liver5.86e-0922
epithelial sac5.86e-0922
digestive gland5.86e-0922
epithelium of foregut-midgut junction5.86e-0922
anatomical boundary5.86e-0922
hepatobiliary system5.86e-0922
foregut-midgut junction5.86e-0922
hepatic diverticulum5.86e-0922
liver primordium5.86e-0922
septum transversum5.86e-0922
liver bud5.86e-0922
subdivision of trunk1.12e-0866
abdomen element1.29e-0849
abdominal segment element1.29e-0849
abdominal segment of trunk1.29e-0849
abdomen1.29e-0849
endoderm-derived structure1.46e-08118
endoderm1.46e-08118
presumptive endoderm1.46e-08118
digestive system1.85e-08116
digestive tract1.85e-08116
primitive gut1.85e-08116
trunk1.94e-0890
gastrointestinal system2.60e-0847
subdivision of digestive tract8.90e-08114
mesenchyme1.49e-0761
entire embryonic mesenchyme1.49e-0761
epithelial tube2.10e-0747
trunk mesenchyme3.58e-0745


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)
MA0003.11.35193
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
MA0028.10.61552
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
MA0055.11.6728
MA0056.10
MA0057.10.337566
MA0058.10.690848
MA0059.11.68104
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
MA0073.16.00139
MA0074.10.911576
MA0076.10.657929
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
MA0091.11.91105
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
MA0116.11.46662
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
MA0145.10.292366
MA0146.11.44443
MA0147.12.34772
MA0148.10.820161
MA0149.10.722227
MA0062.20.412742
MA0035.20.903829
MA0039.22.07301
MA0138.21.07027
MA0002.20.466067
MA0137.20.668025
MA0104.22.10982
MA0047.20.962424
MA0112.20.29236
MA0065.20.292912
MA0150.10.784464
MA0151.10
MA0152.10.962542
MA0153.11.43238
MA0154.10.925147
MA0155.10.840842
MA0156.10.656895
MA0157.11.12772
MA0158.10
MA0159.10.569393
MA0160.10.823568
MA0161.10
MA0162.10.499274
MA0163.10.927936
MA0164.12.15144
MA0080.20.64167
MA0018.20.944669
MA0099.21.06348
MA0079.26.70315
MA0102.22.01714
MA0258.10.520639
MA0259.10.543506
MA0442.10
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