MCL coexpression mm9:859: Difference between revisions
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{{MCL_coexpression_mm9| | 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dehydrogenase (B-specific) activity;0.0163146808650638;105387!GO:0003816;complement component C1s activity;0.0163146808650638;50908!GO:0004301;epoxide hydrolase activity;0.0163146808650638;13849!GO:0004031;aldehyde oxidase activity;0.0163146808650638;11761!GO:0016803;ether hydrolase activity;0.0163146808650638;13849!GO:0016623;oxidoreductase activity, acting on the aldehyde or oxo group of donors, oxygen as acceptor;0.0163146808650638;11761!GO:0004463;leukotriene-A4 hydrolase activity;0.0163146808650638;13849!GO:0016801;hydrolase activity, acting on ether bonds;0.0285413070423536;13849!GO:0030151;molybdenum ion binding;0.0300840475642867;11761!GO:0006805;xenobiotic metabolic process;0.0300840475642867;13849!GO:0019439;aromatic compound catabolic process;0.0300840475642867;13849!GO:0051537;2 iron, 2 sulfur cluster binding;0.0300840475642867;11761!GO:0009410;response to xenobiotic stimulus;0.0300840475642867;13849!GO:0030574;collagen catabolic process;0.0300840475642867;58223!GO:0044259;multicellular organismal macromolecule metabolic process;0.0300840475642867;58223!GO:0044268;multicellular organismal protein metabolic process;0.0300840475642867;58223!GO:0044256;protein digestion;0.0300840475642867;58223!GO:0044254;multicellular organismal protein catabolic process;0.0300840475642867;58223!GO:0044266;multicellular organismal macromolecule catabolic process;0.0300840475642867;58223!GO:0044243;multicellular organismal catabolic process;0.0300840475642867;58223!GO:0032963;collagen metabolic process;0.0300840475642867;58223!GO:0004175;endopeptidase activity;0.0300840475642867;50908,58223!GO:0009636;response to toxin;0.0300840475642867;13849!GO:0044236;multicellular organismal metabolic process;0.0300840475642867;58223!GO:0016229;steroid dehydrogenase activity;0.031913762660244;105387!GO:0051287;NAD binding;0.0321440404871541;11761!GO:0009056;catabolic process;0.0393149711488276;58223,13849!GO:0006958;complement activation, classical pathway;0.0393149711488276;50908!GO:0002455;humoral immune response mediated by circulating immunoglobulin;0.0428880772729188;50908!GO:0006508;proteolysis;0.0428880772729188;50908,58223!GO:0016903;oxidoreductase activity, acting on the aldehyde or oxo group of donors;0.0428880772729188;11761!GO:0005615;extracellular space;0.0428880772729188;50908,58223,13849!GO:0007586;digestion;0.0428880772729188;58223!GO:0006956;complement activation;0.0428880772729188;50908!GO:0002541;activation of plasma proteins during acute inflammatory response;0.0428880772729188;50908!GO:0016787;hydrolase activity;0.0428880772729188;50908,58223,13849!GO:0051536;iron-sulfur cluster binding;0.0428880772729188;11761!GO:0051540;metal cluster binding;0.0428880772729188;11761!GO:0008233;peptidase activity;0.0434545151844588;50908,58223!GO:0044421;extracellular region part;0.0434545151844588;50908,58223,13849!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0005256!1.45e-13!45;UBERON:0002100!4.80e-13!90;UBERON:0000466!5.32e-11!79;UBERON:0005177!1.41e-10!79;UBERON:0003104!1.43e-10!61;UBERON:0009142!1.43e-10!61;UBERON:0009569!2.49e-09!66;UBERON:0002365!8.94e-09!25;UBERON:0002330!8.94e-09!25;UBERON:0003914!1.70e-08!47;UBERON:0002107!5.08e-08!22;UBERON:0007499!5.08e-08!22;UBERON:0006925!5.08e-08!22;UBERON:0009497!5.08e-08!22;UBERON:0000015!5.08e-08!22;UBERON:0002423!5.08e-08!22;UBERON:0006235!5.08e-08!22;UBERON:0008835!5.08e-08!22;UBERON:0003894!5.08e-08!22;UBERON:0004161!5.08e-08!22;UBERON:0008836!5.08e-08!22;UBERON:0005172!7.24e-08!49;UBERON:0005173!7.24e-08!49;UBERON:0002417!7.24e-08!49;UBERON:0000916!7.24e-08!49;UBERON:0009854!1.05e-07!23;UBERON:0009856!1.05e-07!23;UBERON:0000475!4.31e-07!150|tfbs_overrepresentation_for_novel_motifs=0.393008,0.289542,0.367606,0.434198,0.260188,0.448401,0.538088,0.515265,0.181564,0.170907,0.494602,0.526159,0.173454,0.550255,0.756943,0,0.742571,2.00903,1.4996,0.29826,0.883862,0.837949,0.549359,0.717658,0.374936,0.577606,0.909128,0.469052,0.818708,1.23861,0.455168,0.843667,0.250677,0.425071,0.276324,0.185086,0.242032,0.522578,0.221921,0.195877,0.256422,0.460258,0.784847,0.27776,0.983404,0.423266,0.662995,0.484612,1.06276,0.305876,0.725127,0.604356,0.732634,0.985264,1.00271,0.557354,0.314394,0.513517,0.877107,0.555328,0.823643,0.613749,0.560836,0.713876,0.568415,0.754324,1.139,1.48833,0.818971,1.34113,0.349355,0.527912,0.0665967,1.03623,0.140213,0.813951,0.136938,0.651651,0.806481,0.336166,0.179489,0.759925,0.612313,0.167672,0.920903,0.025519,0.0299392,0.757533,0.667883,1.65055,1.20871,0.925879,0.856465,0.265734,0.218233,0.202284,0.982739,0.859272,0.663249,0.681235,0.242106,0.843387,0.967837,0.725721,0.724668,0.459825,0.784351,0.480639,0.340849,0.333829,0.386136,0.96962,0.337254,0.499714,1.21576,0.254749,0.0359654,0.437894,0.743872,0.670977,1.04163,0.692953,0.579418,0.650748,1.26989,0.810177,0.546178,0.849691,1.13749,0.740166,0.950857,0.427043,1.10792,0.570914,1.23736,0.220515,1.03631,0.461647,1.18819,2.01886,1.6187,1.14372,0.591394,0.854131,0.718197,0.460705,0.666107,1.9792,0.403515,0.261837,0.381863,0.0553085,0.986833,0.598134,0.569994,1.06851,0.605358,0.287226,0.39061,0.400939,1.1977,0.920047,0.810622,0.383936,0.714896,0.562634,1.2562,0.524587,0.166768|tfbs_overrepresentation_jaspar=MA0003.1;0.0545917,MA0004.1;1.94256,MA0006.1;0.271714,MA0007.1;0.419994,MA0009.1;0.870101,MA0014.1;0.012738,MA0017.1;0.804572,MA0019.1;0.688051,MA0024.1;0.826339,MA0025.1;1.10341,MA0027.1;2.51754,MA0028.1;0.281528,MA0029.1;0.804619,MA0030.1;0.811181,MA0031.1;0.775627,MA0038.1;0.577528,MA0040.1;0.882616,MA0041.1;0.360875,MA0042.1;0.348174,MA0043.1;0.966833,MA0046.1;0.906029,MA0048.1;0.335404,MA0050.1;0.472794,MA0051.1;1.43259,MA0052.1;0.890676,MA0055.1;0.523649,MA0056.1;0,MA0057.1;0.31126,MA0058.1;0.90507,MA0059.1;1.6636,MA0060.1;0.197678,MA0061.1;0.224905,MA0063.1;0,MA0066.1;0.566617,MA0067.1;1.21448,MA0068.1;0.657844,MA0069.1;0.891016,MA0070.1;0.881319,MA0071.1;0.471969,MA0072.1;0.872842,MA0073.1;0.00296875,MA0074.1;0.531046,MA0076.1;0.315013,MA0077.1;0.851175,MA0078.1;0.61926,MA0081.1;0.375851,MA0083.1;0.96604,MA0084.1;1.54225,MA0087.1;0.922929,MA0088.1;0.49616,MA0089.1;0,MA0090.1;1.03628,MA0091.1;1.98602,MA0092.1;0.401504,MA0093.1;2.19634,MA0095.1;0,MA0098.1;0,MA0100.1;0.519598,MA0101.1;0.362124,MA0103.1;0.307078,MA0105.1;0.133231,MA0106.1;1.51778,MA0107.1;0.301222,MA0108.2;0.710846,MA0109.1;0,MA0111.1;0.415012,MA0113.1;0.598933,MA0114.1;0.222763,MA0115.1;0.969632,MA0116.1;0.27152,MA0117.1;0.937363,MA0119.1;0.951747,MA0122.1;0.957212,MA0124.1;1.16127,MA0125.1;1.0872,MA0130.1;0,MA0131.1;0.683521,MA0132.1;0,MA0133.1;0,MA0135.1;1.00325,MA0136.1;0.550755,MA0139.1;0.169849,MA0140.1;0.519484,MA0141.1;0.869985,MA0142.1;1.79662,MA0143.1;0.615203,MA0144.1;0.640537,MA0145.1;0.246409,MA0146.1;0.636109,MA0147.1;1.24068,MA0148.1;1.14345,MA0149.1;0.367458,MA0062.2;0.137653,MA0035.2;0.524137,MA0039.2;0.402847,MA0138.2;1.61926,MA0002.2;0.172399,MA0137.2;0.32312,MA0104.2;0.54394,MA0047.2;0.576767,MA0112.2;0.2464,MA0065.2;0.247168,MA0150.1;1.89243,MA0151.1;0,MA0152.1;0.576873,MA0153.1;1.01988,MA0154.1;0.677425,MA0155.1;0.275377,MA0156.1;0.314185,MA0157.1;0.729116,MA0158.1;0,MA0159.1;0.688775,MA0160.1;0.453546,MA0161.1;0,MA0162.1;0.230918,MA0163.1;0.408151,MA0164.1;0.551114,MA0080.2;0.302064,MA0018.2;0.560731,MA0099.2;0.669311,MA0079.2;0.0468707,MA0102.2;1.59466,MA0258.1;0.60477,MA0259.1;0.643936,MA0442.1;0}} | ||
Latest revision as of 16:00, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr10:128227959..128228024,+ | p1@Mmp19 |
| Mm9::chr13:4058917..4058918,+ | p@chr13:4058917..4058918 + |
| Mm9::chr1:182926224..182926235,- | p@chr1:182926224..182926235 - |
| Mm9::chr1:182932030..182932048,- | p@chr1:182932030..182932048 - |
| Mm9::chr1:182947620..182947679,- | p1@Ephx1 |
| Mm9::chr1:58086799..58086818,+ | p1@Aox1 |
| Mm9::chr6:124462731..124462753,+ | p1@C1rb |
| Mm9::chr6:124492299..124492325,- | p1@C1s |
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:0047042 | 3-alpha-hydroxysteroid dehydrogenase (B-specific) activity | 0.0163146808650638 |
| GO:0003816 | complement component C1s activity | 0.0163146808650638 |
| GO:0004301 | epoxide hydrolase activity | 0.0163146808650638 |
| GO:0004031 | aldehyde oxidase activity | 0.0163146808650638 |
| GO:0016803 | ether hydrolase activity | 0.0163146808650638 |
| GO:0016623 | oxidoreductase activity, acting on the aldehyde or oxo group of donors, oxygen as acceptor | 0.0163146808650638 |
| GO:0004463 | leukotriene-A4 hydrolase activity | 0.0163146808650638 |
| GO:0016801 | hydrolase activity, acting on ether bonds | 0.0285413070423536 |
| GO:0030151 | molybdenum ion binding | 0.0300840475642867 |
| GO:0006805 | xenobiotic metabolic process | 0.0300840475642867 |
| GO:0019439 | aromatic compound catabolic process | 0.0300840475642867 |
| GO:0051537 | 2 iron, 2 sulfur cluster binding | 0.0300840475642867 |
| GO:0009410 | response to xenobiotic stimulus | 0.0300840475642867 |
| GO:0030574 | collagen catabolic process | 0.0300840475642867 |
| GO:0044259 | multicellular organismal macromolecule metabolic process | 0.0300840475642867 |
| GO:0044268 | multicellular organismal protein metabolic process | 0.0300840475642867 |
| GO:0044256 | protein digestion | 0.0300840475642867 |
| GO:0044254 | multicellular organismal protein catabolic process | 0.0300840475642867 |
| GO:0044266 | multicellular organismal macromolecule catabolic process | 0.0300840475642867 |
| GO:0044243 | multicellular organismal catabolic process | 0.0300840475642867 |
| GO:0032963 | collagen metabolic process | 0.0300840475642867 |
| GO:0004175 | endopeptidase activity | 0.0300840475642867 |
| GO:0009636 | response to toxin | 0.0300840475642867 |
| GO:0044236 | multicellular organismal metabolic process | 0.0300840475642867 |
| GO:0016229 | steroid dehydrogenase activity | 0.031913762660244 |
| GO:0051287 | NAD binding | 0.0321440404871541 |
| GO:0009056 | catabolic process | 0.0393149711488276 |
| GO:0006958 | complement activation, classical pathway | 0.0393149711488276 |
| GO:0002455 | humoral immune response mediated by circulating immunoglobulin | 0.0428880772729188 |
| GO:0006508 | proteolysis | 0.0428880772729188 |
| GO:0016903 | oxidoreductase activity, acting on the aldehyde or oxo group of donors | 0.0428880772729188 |
| GO:0005615 | extracellular space | 0.0428880772729188 |
| GO:0007586 | digestion | 0.0428880772729188 |
| GO:0006956 | complement activation | 0.0428880772729188 |
| GO:0002541 | activation of plasma proteins during acute inflammatory response | 0.0428880772729188 |
| GO:0016787 | hydrolase activity | 0.0428880772729188 |
| GO:0051536 | iron-sulfur cluster binding | 0.0428880772729188 |
| GO:0051540 | metal cluster binding | 0.0428880772729188 |
| GO:0008233 | peptidase activity | 0.0434545151844588 |
| GO:0044421 | extracellular region part | 0.0434545151844588 |
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 |
|---|---|---|
| trunk mesenchyme | 1.45e-13 | 45 |
| trunk | 4.80e-13 | 90 |
| immaterial anatomical entity | 5.32e-11 | 79 |
| trunk region element | 1.41e-10 | 79 |
| mesenchyme | 1.43e-10 | 61 |
| entire embryonic mesenchyme | 1.43e-10 | 61 |
| subdivision of trunk | 2.49e-09 | 66 |
| exocrine gland | 8.94e-09 | 25 |
| exocrine system | 8.94e-09 | 25 |
| epithelial tube | 1.70e-08 | 47 |
| liver | 5.08e-08 | 22 |
| epithelial sac | 5.08e-08 | 22 |
| digestive gland | 5.08e-08 | 22 |
| epithelium of foregut-midgut junction | 5.08e-08 | 22 |
| anatomical boundary | 5.08e-08 | 22 |
| hepatobiliary system | 5.08e-08 | 22 |
| foregut-midgut junction | 5.08e-08 | 22 |
| hepatic diverticulum | 5.08e-08 | 22 |
| liver primordium | 5.08e-08 | 22 |
| septum transversum | 5.08e-08 | 22 |
| liver bud | 5.08e-08 | 22 |
| abdomen element | 7.24e-08 | 49 |
| abdominal segment element | 7.24e-08 | 49 |
| abdominal segment of trunk | 7.24e-08 | 49 |
| abdomen | 7.24e-08 | 49 |
| digestive tract diverticulum | 1.05e-07 | 23 |
| sac | 1.05e-07 | 23 |
| organism subdivision | 4.31e-07 | 150 |
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 | 0.0545917 |
| MA0004.1 | 1.94256 |
| MA0006.1 | 0.271714 |
| MA0007.1 | 0.419994 |
| MA0009.1 | 0.870101 |
| MA0014.1 | 0.012738 |
| MA0017.1 | 0.804572 |
| MA0019.1 | 0.688051 |
| MA0024.1 | 0.826339 |
| MA0025.1 | 1.10341 |
| MA0027.1 | 2.51754 |
| MA0028.1 | 0.281528 |
| MA0029.1 | 0.804619 |
| MA0030.1 | 0.811181 |
| MA0031.1 | 0.775627 |
| MA0038.1 | 0.577528 |
| MA0040.1 | 0.882616 |
| MA0041.1 | 0.360875 |
| MA0042.1 | 0.348174 |
| MA0043.1 | 0.966833 |
| MA0046.1 | 0.906029 |
| MA0048.1 | 0.335404 |
| MA0050.1 | 0.472794 |
| MA0051.1 | 1.43259 |
| MA0052.1 | 0.890676 |
| MA0055.1 | 0.523649 |
| MA0056.1 | 0 |
| MA0057.1 | 0.31126 |
| MA0058.1 | 0.90507 |
| MA0059.1 | 1.6636 |
| MA0060.1 | 0.197678 |
| MA0061.1 | 0.224905 |
| MA0063.1 | 0 |
| MA0066.1 | 0.566617 |
| MA0067.1 | 1.21448 |
| MA0068.1 | 0.657844 |
| MA0069.1 | 0.891016 |
| MA0070.1 | 0.881319 |
| MA0071.1 | 0.471969 |
| MA0072.1 | 0.872842 |
| MA0073.1 | 0.00296875 |
| MA0074.1 | 0.531046 |
| MA0076.1 | 0.315013 |
| MA0077.1 | 0.851175 |
| MA0078.1 | 0.61926 |
| MA0081.1 | 0.375851 |
| MA0083.1 | 0.96604 |
| MA0084.1 | 1.54225 |
| MA0087.1 | 0.922929 |
| MA0088.1 | 0.49616 |
| MA0089.1 | 0 |
| MA0090.1 | 1.03628 |
| MA0091.1 | 1.98602 |
| MA0092.1 | 0.401504 |
| MA0093.1 | 2.19634 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.519598 |
| MA0101.1 | 0.362124 |
| MA0103.1 | 0.307078 |
| MA0105.1 | 0.133231 |
| MA0106.1 | 1.51778 |
| MA0107.1 | 0.301222 |
| MA0108.2 | 0.710846 |
| MA0109.1 | 0 |
| MA0111.1 | 0.415012 |
| MA0113.1 | 0.598933 |
| MA0114.1 | 0.222763 |
| MA0115.1 | 0.969632 |
| MA0116.1 | 0.27152 |
| MA0117.1 | 0.937363 |
| MA0119.1 | 0.951747 |
| MA0122.1 | 0.957212 |
| MA0124.1 | 1.16127 |
| MA0125.1 | 1.0872 |
| MA0130.1 | 0 |
| MA0131.1 | 0.683521 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.00325 |
| MA0136.1 | 0.550755 |
| MA0139.1 | 0.169849 |
| MA0140.1 | 0.519484 |
| MA0141.1 | 0.869985 |
| MA0142.1 | 1.79662 |
| MA0143.1 | 0.615203 |
| MA0144.1 | 0.640537 |
| MA0145.1 | 0.246409 |
| MA0146.1 | 0.636109 |
| MA0147.1 | 1.24068 |
| MA0148.1 | 1.14345 |
| MA0149.1 | 0.367458 |
| MA0062.2 | 0.137653 |
| MA0035.2 | 0.524137 |
| MA0039.2 | 0.402847 |
| MA0138.2 | 1.61926 |
| MA0002.2 | 0.172399 |
| MA0137.2 | 0.32312 |
| MA0104.2 | 0.54394 |
| MA0047.2 | 0.576767 |
| MA0112.2 | 0.2464 |
| MA0065.2 | 0.247168 |
| MA0150.1 | 1.89243 |
| MA0151.1 | 0 |
| MA0152.1 | 0.576873 |
| MA0153.1 | 1.01988 |
| MA0154.1 | 0.677425 |
| MA0155.1 | 0.275377 |
| MA0156.1 | 0.314185 |
| MA0157.1 | 0.729116 |
| MA0158.1 | 0 |
| MA0159.1 | 0.688775 |
| MA0160.1 | 0.453546 |
| MA0161.1 | 0 |
| MA0162.1 | 0.230918 |
| MA0163.1 | 0.408151 |
| MA0164.1 | 0.551114 |
| MA0080.2 | 0.302064 |
| MA0018.2 | 0.560731 |
| MA0099.2 | 0.669311 |
| MA0079.2 | 0.0468707 |
| MA0102.2 | 1.59466 |
| MA0258.1 | 0.60477 |
| MA0259.1 | 0.643936 |
| MA0442.1 | 0 |
