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 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|tfbs_overrepresentation_jaspar=MA0003.1;1.35193,MA0004.1;0.801718,MA0006.1;0.60285,MA0007.1;0.784593,MA0009.1;1.27673,MA0014.1;0.416365,MA0017.1;0.635031,MA0019.1;1.08369,MA0024.1;1.23079,MA0025.1;1.51835,MA0027.1;2.9431,MA0028.1;0.61552,MA0029.1;1.20789,MA0030.1;1.21482,MA0031.1;1.17722,MA0038.1;0.963265,MA0040.1;1.28983,MA0041.1;0.714279,MA0042.1;0.69885,MA0043.1;1.3775,MA0046.1;1.31428,MA0048.1;1.66457,MA0050.1;0.845669,MA0051.1;0.973068,MA0052.1;1.29825,MA0055.1;1.6728,MA0056.1;0,MA0057.1;0.337566,MA0058.1;0.690848,MA0059.1;1.68104,MA0060.1;0.502699,MA0061.1;0.5406,MA0063.1;0,MA0066.1;0.951196,MA0067.1;1.63197,MA0068.1;0.343188,MA0069.1;1.29861,MA0070.1;1.28847,MA0071.1;0.844726,MA0072.1;1.2796,MA0073.1;6.00139,MA0074.1;0.911576,MA0076.1;0.657929,MA0077.1;1.2569,MA0078.1;1.0091,MA0081.1;0.732313,MA0083.1;1.37668,MA0084.1;1.96428,MA0087.1;1.33189,MA0088.1;0.27999,MA0089.1;0,MA0090.1;0.762482,MA0091.1;1.91105,MA0092.1;0.762845,MA0093.1;0.62555,MA0095.1;0,MA0098.1;0,MA0100.1;0.89873,MA0101.1;0.71579,MA0103.1;0.647985,MA0105.1;0.405648,MA0106.1;1.01755,MA0107.1;0.640607,MA0108.2;1.10817,MA0109.1;0,MA0111.1;0.778753,MA0113.1;0.986839,MA0114.1;0.537669,MA0115.1;1.38041,MA0116.1;1.46662,MA0117.1;1.34691,MA0119.1;0.716476,MA0122.1;1.36752,MA0124.1;1.57762,MA0125.1;1.5017,MA0130.1;0,MA0131.1;1.07881,MA0132.1;0,MA0133.1;0,MA0135.1;1.4152,MA0136.1;0.933582,MA0139.1;0.462282,MA0140.1;0.898603,MA0141.1;0.671467,MA0142.1;1.16183,MA0143.1;1.00467,MA0144.1;0.541532,MA0145.1;0.292366,MA0146.1;1.44443,MA0147.1;2.34772,MA0148.1;0.820161,MA0149.1;0.722227,MA0062.2;0.412742,MA0035.2;0.903829,MA0039.2;2.07301,MA0138.2;1.07027,MA0002.2;0.466067,MA0137.2;0.668025,MA0104.2;2.10982,MA0047.2;0.962424,MA0112.2;0.29236,MA0065.2;0.292912,MA0150.1;0.784464,MA0151.1;0,MA0152.1;0.962542,MA0153.1;1.43238,MA0154.1;0.925147,MA0155.1;0.840842,MA0156.1;0.656895,MA0157.1;1.12772,MA0158.1;0,MA0159.1;0.569393,MA0160.1;0.823568,MA0161.1;0,MA0162.1;0.499274,MA0163.1;0.927936,MA0164.1;2.15144,MA0080.2;0.64167,MA0018.2;0.944669,MA0099.2;1.06348,MA0079.2;6.70315,MA0102.2;2.01714,MA0258.1;0.520639,MA0259.1;0.543506,MA0442.1;0}} | ||
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 ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0030350 | iron-responsive element binding | 0.00964198644664237 |
| GO:0003994 | aconitate hydratase activity | 0.00964198644664237 |
| GO:0006091 | generation of precursor metabolites and energy | 0.0146926514014748 |
| GO:0003995 | acyl-CoA dehydrogenase activity | 0.0218360101574241 |
| GO:0051539 | 4 iron, 4 sulfur cluster binding | 0.0218360101574241 |
| GO:0055072 | iron ion homeostasis | 0.0218360101574241 |
| GO:0006099 | tricarboxylic acid cycle | 0.0218360101574241 |
| GO:0006879 | cellular iron ion homeostasis | 0.0218360101574241 |
| GO:0046356 | acetyl-CoA catabolic process | 0.0218360101574241 |
| GO:0009060 | aerobic respiration | 0.0218360101574241 |
| GO:0009109 | coenzyme catabolic process | 0.0218360101574241 |
| GO:0045333 | cellular respiration | 0.0218360101574241 |
| GO:0003729 | mRNA binding | 0.0218360101574241 |
| GO:0051187 | cofactor catabolic process | 0.0218360101574241 |
| GO:0006084 | acetyl-CoA metabolic process | 0.0218360101574241 |
| GO:0016627 | oxidoreductase activity, acting on the CH-CH group of donors | 0.0230077630181863 |
| GO:0051536 | iron-sulfur cluster binding | 0.0230077630181863 |
| GO:0051540 | metal cluster binding | 0.0230077630181863 |
| GO:0016836 | hydro-lyase activity | 0.0248341587454829 |
| GO:0050660 | FAD binding | 0.0270470899900274 |
| GO:0016835 | carbon-oxygen lyase activity | 0.0270470899900274 |
| GO:0015980 | energy derivation by oxidation of organic compounds | 0.0288752440179602 |
| GO:0042579 | microbody | 0.0352706574318195 |
| GO:0005777 | peroxisome | 0.0352706574318195 |
| GO:0030005 | cellular di-, tri-valent inorganic cation homeostasis | 0.0362472931151761 |
| GO:0055066 | di-, tri-valent inorganic cation homeostasis | 0.0362472931151761 |
| GO:0030003 | cellular cation homeostasis | 0.0367401753938845 |
| GO:0055080 | cation homeostasis | 0.0367401753938845 |
| GO:0050662 | coenzyme binding | 0.0384474968968982 |
| GO:0006417 | regulation of translation | 0.0419545494583387 |
| GO:0031326 | regulation of cellular biosynthetic process | 0.0424022794648206 |
| GO:0055082 | cellular chemical homeostasis | 0.0424022794648206 |
| GO:0006873 | cellular ion homeostasis | 0.0424022794648206 |
| GO:0016829 | lyase activity | 0.0424022794648206 |
| GO:0009889 | regulation of biosynthetic process | 0.0424022794648206 |
| GO:0006732 | coenzyme metabolic process | 0.0424022794648206 |
| GO:0050801 | ion homeostasis | 0.0424338769084272 |
| GO:0048037 | cofactor binding | 0.0424338769084272 |
| GO:0051186 | cofactor metabolic process | 0.0459977810919878 |
| GO:0048878 | chemical homeostasis | 0.0493368470455996 |
| GO:0019725 | cellular homeostasis | 0.0493368470455996 |
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>
| Ontology term | p-value | n |
|---|---|---|
| exocrine gland | 2.26e-10 | 25 |
| exocrine system | 2.26e-10 | 25 |
| intestine | 2.45e-10 | 31 |
| trunk region element | 1.06e-09 | 79 |
| digestive tract diverticulum | 2.09e-09 | 23 |
| sac | 2.09e-09 | 23 |
| liver | 5.86e-09 | 22 |
| epithelial sac | 5.86e-09 | 22 |
| digestive gland | 5.86e-09 | 22 |
| epithelium of foregut-midgut junction | 5.86e-09 | 22 |
| anatomical boundary | 5.86e-09 | 22 |
| hepatobiliary system | 5.86e-09 | 22 |
| foregut-midgut junction | 5.86e-09 | 22 |
| hepatic diverticulum | 5.86e-09 | 22 |
| liver primordium | 5.86e-09 | 22 |
| septum transversum | 5.86e-09 | 22 |
| liver bud | 5.86e-09 | 22 |
| subdivision of trunk | 1.12e-08 | 66 |
| abdomen element | 1.29e-08 | 49 |
| abdominal segment element | 1.29e-08 | 49 |
| abdominal segment of trunk | 1.29e-08 | 49 |
| abdomen | 1.29e-08 | 49 |
| endoderm-derived structure | 1.46e-08 | 118 |
| endoderm | 1.46e-08 | 118 |
| presumptive endoderm | 1.46e-08 | 118 |
| digestive system | 1.85e-08 | 116 |
| digestive tract | 1.85e-08 | 116 |
| primitive gut | 1.85e-08 | 116 |
| trunk | 1.94e-08 | 90 |
| gastrointestinal system | 2.60e-08 | 47 |
| subdivision of digestive tract | 8.90e-08 | 114 |
| mesenchyme | 1.49e-07 | 61 |
| entire embryonic mesenchyme | 1.49e-07 | 61 |
| epithelial tube | 2.10e-07 | 47 |
| trunk mesenchyme | 3.58e-07 | 45 |
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) |
|---|---|
| MA0003.1 | 1.35193 |
| MA0004.1 | 0.801718 |
| MA0006.1 | 0.60285 |
| MA0007.1 | 0.784593 |
| MA0009.1 | 1.27673 |
| MA0014.1 | 0.416365 |
| MA0017.1 | 0.635031 |
| MA0019.1 | 1.08369 |
| MA0024.1 | 1.23079 |
| MA0025.1 | 1.51835 |
| MA0027.1 | 2.9431 |
| MA0028.1 | 0.61552 |
| MA0029.1 | 1.20789 |
| MA0030.1 | 1.21482 |
| MA0031.1 | 1.17722 |
| MA0038.1 | 0.963265 |
| MA0040.1 | 1.28983 |
| MA0041.1 | 0.714279 |
| MA0042.1 | 0.69885 |
| MA0043.1 | 1.3775 |
| MA0046.1 | 1.31428 |
| MA0048.1 | 1.66457 |
| MA0050.1 | 0.845669 |
| MA0051.1 | 0.973068 |
| MA0052.1 | 1.29825 |
| MA0055.1 | 1.6728 |
| MA0056.1 | 0 |
| MA0057.1 | 0.337566 |
| MA0058.1 | 0.690848 |
| MA0059.1 | 1.68104 |
| MA0060.1 | 0.502699 |
| MA0061.1 | 0.5406 |
| MA0063.1 | 0 |
| MA0066.1 | 0.951196 |
| MA0067.1 | 1.63197 |
| MA0068.1 | 0.343188 |
| MA0069.1 | 1.29861 |
| MA0070.1 | 1.28847 |
| MA0071.1 | 0.844726 |
| MA0072.1 | 1.2796 |
| MA0073.1 | 6.00139 |
| MA0074.1 | 0.911576 |
| MA0076.1 | 0.657929 |
| MA0077.1 | 1.2569 |
| MA0078.1 | 1.0091 |
| MA0081.1 | 0.732313 |
| MA0083.1 | 1.37668 |
| MA0084.1 | 1.96428 |
| MA0087.1 | 1.33189 |
| MA0088.1 | 0.27999 |
| MA0089.1 | 0 |
| MA0090.1 | 0.762482 |
| MA0091.1 | 1.91105 |
| MA0092.1 | 0.762845 |
| MA0093.1 | 0.62555 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.89873 |
| MA0101.1 | 0.71579 |
| MA0103.1 | 0.647985 |
| MA0105.1 | 0.405648 |
| MA0106.1 | 1.01755 |
| MA0107.1 | 0.640607 |
| MA0108.2 | 1.10817 |
| MA0109.1 | 0 |
| MA0111.1 | 0.778753 |
| MA0113.1 | 0.986839 |
| MA0114.1 | 0.537669 |
| MA0115.1 | 1.38041 |
| MA0116.1 | 1.46662 |
| MA0117.1 | 1.34691 |
| MA0119.1 | 0.716476 |
| MA0122.1 | 1.36752 |
| MA0124.1 | 1.57762 |
| MA0125.1 | 1.5017 |
| MA0130.1 | 0 |
| MA0131.1 | 1.07881 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.4152 |
| MA0136.1 | 0.933582 |
| MA0139.1 | 0.462282 |
| MA0140.1 | 0.898603 |
| MA0141.1 | 0.671467 |
| MA0142.1 | 1.16183 |
| MA0143.1 | 1.00467 |
| MA0144.1 | 0.541532 |
| MA0145.1 | 0.292366 |
| MA0146.1 | 1.44443 |
| MA0147.1 | 2.34772 |
| MA0148.1 | 0.820161 |
| MA0149.1 | 0.722227 |
| MA0062.2 | 0.412742 |
| MA0035.2 | 0.903829 |
| MA0039.2 | 2.07301 |
| MA0138.2 | 1.07027 |
| MA0002.2 | 0.466067 |
| MA0137.2 | 0.668025 |
| MA0104.2 | 2.10982 |
| MA0047.2 | 0.962424 |
| MA0112.2 | 0.29236 |
| MA0065.2 | 0.292912 |
| MA0150.1 | 0.784464 |
| MA0151.1 | 0 |
| MA0152.1 | 0.962542 |
| MA0153.1 | 1.43238 |
| MA0154.1 | 0.925147 |
| MA0155.1 | 0.840842 |
| MA0156.1 | 0.656895 |
| MA0157.1 | 1.12772 |
| MA0158.1 | 0 |
| MA0159.1 | 0.569393 |
| MA0160.1 | 0.823568 |
| MA0161.1 | 0 |
| MA0162.1 | 0.499274 |
| MA0163.1 | 0.927936 |
| MA0164.1 | 2.15144 |
| MA0080.2 | 0.64167 |
| MA0018.2 | 0.944669 |
| MA0099.2 | 1.06348 |
| MA0079.2 | 6.70315 |
| MA0102.2 | 2.01714 |
| MA0258.1 | 0.520639 |
| MA0259.1 | 0.543506 |
| MA0442.1 | 0 |
