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MCL coexpression mm9:739: Difference between revisions

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{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0047115;trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity;0.0154495151481948;71755!GO:0004034;aldose 1-epimerase activity;0.0154495151481948;319625!GO:0016151;nickel ion binding;0.0411817804150184;12350!GO:0004679;AMP-activated protein kinase activity;0.0432231042462781;108099!GO:0016857;racemase and epimerase activity, acting on carbohydrates and derivatives;0.0432231042462781;319625!
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|ontology_enrichment_uberon=UBERON:0002365!3.28e-10!25;UBERON:0002330!3.28e-10!25;UBERON:0002107!9.72e-10!22;UBERON:0007499!9.72e-10!22;UBERON:0006925!9.72e-10!22;UBERON:0009497!9.72e-10!22;UBERON:0000015!9.72e-10!22;UBERON:0002423!9.72e-10!22;UBERON:0006235!9.72e-10!22;UBERON:0008835!9.72e-10!22;UBERON:0003894!9.72e-10!22;UBERON:0004161!9.72e-10!22;UBERON:0008836!9.72e-10!22;UBERON:0009854!5.20e-09!23;UBERON:0009856!5.20e-09!23;UBERON:0005172!1.33e-08!49;UBERON:0005173!1.33e-08!49;UBERON:0002417!1.33e-08!49;UBERON:0000916!1.33e-08!49;UBERON:0003104!7.31e-08!61;UBERON:0009142!7.31e-08!61;UBERON:0005256!9.43e-08!45;UBERON:0003914!1.17e-07!47;UBERON:0009569!2.18e-07!66;UBERON:0005177!4.92e-07!79
|tfbs_overrepresentation_for_novel_motifs=0.321524,0.588611,0.297937,0.360062,0.580303,0.373426,0.458558,0.124431,0.131493,0.10445,0.417132,0.447169,0.124608,0.470194,0.613681,0,0.656089,0.19356,1.209,0.205418,0.26524,0.336916,0.469335,0.198877,0.304728,0.496413,1.71373,0.392919,0.238759,0.572447,0.379806,0.754912,0.560002,0.31333,0.614653,4.4587,0.184038,0.443753,0.963289,0.143746,0.196807,0.38461,0.307718,0.215898,0.434259,0.349801,0.578773,0.407653,0.104497,0.677281,0.639101,0.522137,0.0747297,0.894161,0.911367,0.47699,0.249055,0.435119,0.101408,0.47505,0.735292,0.531188,0.854737,0.628155,0.487593,0.667546,1.04613,1.3932,0.730718,1.24673,0.281085,0.80439,0.03967,0.944464,0.659328,1.04341,0.0942164,0.567793,0.718494,0.268962,0.406536,1.61386,0.529804,0.380754,0.830765,0.0122854,0.0697823,1.44534,0.583509,1.55487,1.11522,0.835661,0.767462,1.11849,0.163126,0.455999,0.388243,0.770215,0.57902,0.86751,0.541671,0.754637,0.87698,0.639679,0.638654,0.3842,0.696857,0.403887,0.273261,0.266818,0.315128,0.878738,0.743427,0.421988,1.12221,0.5687,0.993542,0.363536,0.657356,0.534159,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,0.466292,0.760818,1.04463,0.59809,0.86025,0.353344,1.01535,0.48999,1.14365,0.142597,0.329172,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,0.385031,0.581788,1.88287,0.882109,0.201635,0.580497,0.0316649,0.895708,0.46758,0.489108,0.976367,0.523103,0.224422,0.319291,0.328917,1.1043,0.829923,0.722546,0.313083,0.629147,0.482049,0.53929,0.445669,0.0300841
|tfbs_overrepresentation_jaspar=MA0003.1;0.347165,MA0004.1;0.360508,MA0006.1;0.210471,MA0007.1;0.346734,MA0009.1;0.780842,MA0014.1;1.80909,MA0017.1;0.233089,MA0019.1;0.603066,MA0024.1;0.737933,MA0025.1;1.01089,MA0027.1;2.42079,MA0028.1;0.625707,MA0029.1;0.716673,MA0030.1;0.723093,MA0031.1;0.688336,MA0038.1;0.496338,MA0040.1;0.79313,MA0041.1;0.291712,MA0042.1;0.279998,MA0043.1;0.875991,MA0046.1;0.816137,MA0048.1;0.509074,MA0050.1;0.396459,MA0051.1;0.504875,MA0052.1;0.801048,MA0055.1;0.344,MA0056.1;0,MA0057.1;1.73264,MA0058.1;0.273976,MA0059.1;0.28489,MA0060.1;0.145297,MA0061.1;0.504772,MA0063.1;0,MA0066.1;0.485868,MA0067.1;1.12095,MA0068.1;0.22316,MA0069.1;0.801381,MA0070.1;0.791856,MA0071.1;0.395679,MA0072.1;0.783532,MA0073.1;7.9919e-07,MA0074.1;0.451832,MA0076.1;0.696577,MA0077.1;0.762273,MA0078.1;0.536502,MA0081.1;0.305576,MA0083.1;3.35813,MA0084.1;1.44691,MA0087.1;0.832758,MA0088.1;0.14959,MA0089.1;0,MA0090.1;0.329158,MA0091.1;0.973668,MA0092.1;0.877917,MA0093.1;0.226349,MA0095.1;0,MA0098.1;0,MA0100.1;0.440912,MA0101.1;0.292867,MA0103.1;0.242398,MA0105.1;0.0911942,MA0106.1;0.543967,MA0107.1;0.237082,MA0108.2;0.625209,MA0109.1;0,MA0111.1;0.90605,MA0113.1;0.516916,MA0114.1;1.53894,MA0115.1;0.878749,MA0116.1;0.210297,MA0117.1;0.846964,MA0119.1;0.293392,MA0122.1;0.866511,MA0124.1;1.06819,MA0125.1;0.994853,MA0130.1;0,MA0131.1;0.598671,MA0132.1;0,MA0133.1;0,MA0135.1;0.911905,MA0136.1;0.470672,MA0139.1;0.121562,MA0140.1;0.440804,MA0141.1;0.259554,MA0142.1;0.674191,MA0143.1;0.53259,MA0144.1;0.506239,MA0145.1;1.46364,MA0146.1;0.111454,MA0147.1;0.179496,MA0148.1;0.375491,MA0149.1;0.2978,MA0062.2;0.314778,MA0035.2;0.44524,MA0039.2;0.00879115,MA0138.2;0.590987,MA0002.2;0.123715,MA0137.2;0.257017,MA0104.2;0.134457,MA0047.2;0.495607,MA0112.2;0.0422488,MA0065.2;1.9594,MA0150.1;0.346631,MA0151.1;0,MA0152.1;0.495709,MA0153.1;0.92832,MA0154.1;0.232525,MA0155.1;0.416651,MA0156.1;0.248865,MA0157.1;0.642984,MA0158.1;0,MA0159.1;3.9579,MA0160.1;0.378276,MA0161.1;0,MA0162.1;0.730425,MA0163.1;0.971627,MA0164.1;0.471016,MA0080.2;0.237846,MA0018.2;0.480226,MA0099.2;0.584892,MA0079.2;1.09834,MA0102.2;1.49914,MA0258.1;0.156336,MA0259.1;0.50935,MA0442.1;0
}}

Latest revision as of 15:48, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr17:80527211..80527214,+p@chr17:80527211..80527214
+
Mm9::chr1:152313321..152313366,-p1@Prg4
Mm9::chr3:14863428..14863446,+p4@Car3
Mm9::chr3:14863451..14863467,+p2@Car3
Mm9::chr5:24606442..24606475,-p2@Prkag2
Mm9::chr7:147946643..147946679,-p@chr7:147946643..147946679
-
Mm9::chr7:28377746..28377764,+p9@Akt2
Mm9::chr7:28377795..28377809,+p10@Akt2
Mm9::chr7:52744144..52744172,-p1@Dhdh
Mm9::chr7:52744205..52744230,-p2@Dhdh


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:0047115trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity0.0154495151481948
GO:0004034aldose 1-epimerase activity0.0154495151481948
GO:0016151nickel ion binding0.0411817804150184
GO:0004679AMP-activated protein kinase activity0.0432231042462781
GO:0016857racemase and epimerase activity, acting on carbohydrates and derivatives0.0432231042462781



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>


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)
MA0003.10.347165
MA0004.10.360508
MA0006.10.210471
MA0007.10.346734
MA0009.10.780842
MA0014.11.80909
MA0017.10.233089
MA0019.10.603066
MA0024.10.737933
MA0025.11.01089
MA0027.12.42079
MA0028.10.625707
MA0029.10.716673
MA0030.10.723093
MA0031.10.688336
MA0038.10.496338
MA0040.10.79313
MA0041.10.291712
MA0042.10.279998
MA0043.10.875991
MA0046.10.816137
MA0048.10.509074
MA0050.10.396459
MA0051.10.504875
MA0052.10.801048
MA0055.10.344
MA0056.10
MA0057.11.73264
MA0058.10.273976
MA0059.10.28489
MA0060.10.145297
MA0061.10.504772
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.10.22316
MA0069.10.801381
MA0070.10.791856
MA0071.10.395679
MA0072.10.783532
MA0073.17.9919e-07
MA0074.10.451832
MA0076.10.696577
MA0077.10.762273
MA0078.10.536502
MA0081.10.305576
MA0083.13.35813
MA0084.11.44691
MA0087.10.832758
MA0088.10.14959
MA0089.10
MA0090.10.329158
MA0091.10.973668
MA0092.10.877917
MA0093.10.226349
MA0095.10
MA0098.10
MA0100.10.440912
MA0101.10.292867
MA0103.10.242398
MA0105.10.0911942
MA0106.10.543967
MA0107.10.237082
MA0108.20.625209
MA0109.10
MA0111.10.90605
MA0113.10.516916
MA0114.11.53894
MA0115.10.878749
MA0116.10.210297
MA0117.10.846964
MA0119.10.293392
MA0122.10.866511
MA0124.11.06819
MA0125.10.994853
MA0130.10
MA0131.10.598671
MA0132.10
MA0133.10
MA0135.10.911905
MA0136.10.470672
MA0139.10.121562
MA0140.10.440804
MA0141.10.259554
MA0142.10.674191
MA0143.10.53259
MA0144.10.506239
MA0145.11.46364
MA0146.10.111454
MA0147.10.179496
MA0148.10.375491
MA0149.10.2978
MA0062.20.314778
MA0035.20.44524
MA0039.20.00879115
MA0138.20.590987
MA0002.20.123715
MA0137.20.257017
MA0104.20.134457
MA0047.20.495607
MA0112.20.0422488
MA0065.21.9594
MA0150.10.346631
MA0151.10
MA0152.10.495709
MA0153.10.92832
MA0154.10.232525
MA0155.10.416651
MA0156.10.248865
MA0157.10.642984
MA0158.10
MA0159.13.9579
MA0160.10.378276
MA0161.10
MA0162.10.730425
MA0163.10.971627
MA0164.10.471016
MA0080.20.237846
MA0018.20.480226
MA0099.20.584892
MA0079.21.09834
MA0102.21.49914
MA0258.10.156336
MA0259.10.50935
MA0442.10
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