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MCL coexpression mm9:699: Difference between revisions

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{{MCL_coexpression_mm9
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|tfbs_overrepresentation_for_novel_motifs=0.321524,0.0683387,0.297937,0.360062,0.200163,0.373426,0.458558,0.392928,0.411053,0.0244487,0.417132,0.447169,0.124608,0.470194,0.214197,0,0.656089,0.19356,0.113609,0.451901,0.26524,0.336916,0.469335,0.198877,0.304728,0.496413,0.107695,0.392919,0.238759,0.271461,0.379806,0.754912,0.191698,0.0942651,0.214608,0.0351598,0.184038,0.443753,0.166348,0.143746,0.572271,0.38461,0.307718,0.215898,0.119503,0.349801,0.578773,0.407653,1.53869,0.241306,0.639101,0.522137,0.259389,0.894161,0.911367,0.47699,0.249055,0.435119,0.332535,0.47505,0.735292,0.531188,0.433822,0.628155,0.487593,0.667546,1.04613,1.3932,1.73371,1.24673,0.281085,0.80439,0.03967,0.944464,0.0968968,0.0893951,0.0942164,0.567793,0.718494,0.74114,1.31277,0.673009,2.25921,0.380754,0.830765,0.0122854,4.8863,0.0791202,0.583509,1.55487,1.11522,0.835661,0.767462,0.205117,0.163126,0.455999,0.122617,0.770215,0.57902,0.0659594,1.03532,0.754637,0.87698,0.639679,0.638654,0.3842,0.696857,1.04215,0.273261,0.266818,0.315128,0.878738,0.26996,0.421988,1.12221,0.5687,0.0187247,0.363536,0.657356,0.181004,0.949798,1.47759,0.498153,0.566919,1.17594,0.722111,0.466292,0.760818,1.04463,0.207624,0.86025,0.931072,1.01535,0.48999,1.14365,0.0358067,0.877308,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,0.385031,1.42284,1.88287,0.331322,0.201635,0.580497,0.0316649,0.895708,0.153911,0.489108,0.976367,0.523103,0.224422,0.855195,0.328917,1.1043,0.829923,0.722546,0.313083,1.52228,0.482049,0.18312,0.445669,0.0300841
}}

Latest revision as of 15:44, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:109856955..109856967,-p5@Abca8b
Mm9::chr14:57239396..57239401,-p2@ENSMUST00000161382
p2@ENSMUST00000162231
Mm9::chr16:31168077..31168081,-p@chr16:31168077..31168081
-
Mm9::chr19:39815489..39815518,-p@chr19:39815489..39815518
-
Mm9::chr19:46743077..46743093,+p@chr19:46743077..46743093
+
Mm9::chr3:6802683..6802687,-p@chr3:6802683..6802687
-
Mm9::chr3:82812587..82812624,-p@chr3:82812587..82812624
-
Mm9::chrX:147028881..147028901,+p5@Pfkfb1
Mm9::chrX:147028936..147028956,+p4@Pfkfb1
Mm9::chrX:147028963..147028989,+p3@Pfkfb1


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:0004331fructose-2,6-bisphosphate 2-phosphatase activity0.0160212513531023
GO:00038736-phosphofructo-2-kinase activity0.0160212513531023
GO:0006003fructose 2,6-bisphosphate metabolic process0.0160212513531023
GO:0006000fructose metabolic process0.0160212513531023
GO:0008443phosphofructokinase activity0.0192212882000167
GO:0019203carbohydrate phosphatase activity0.0192212882000167



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
liver1.10e-2422
epithelial sac1.10e-2422
digestive gland1.10e-2422
epithelium of foregut-midgut junction1.10e-2422
anatomical boundary1.10e-2422
hepatobiliary system1.10e-2422
foregut-midgut junction1.10e-2422
hepatic diverticulum1.10e-2422
liver primordium1.10e-2422
septum transversum1.10e-2422
liver bud1.10e-2422
digestive tract diverticulum2.53e-2323
sac2.53e-2323
exocrine gland6.25e-2125
exocrine system6.25e-2125
trunk mesenchyme5.79e-1345
abdomen element2.48e-1149
abdominal segment element2.48e-1149
abdominal segment of trunk2.48e-1149
abdomen2.48e-1149
epithelial tube5.21e-1047
endocrine gland5.01e-0860
mesenchyme8.65e-0861
entire embryonic mesenchyme8.65e-0861
gland6.38e-0765


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)
MA0003.10.00561553
MA0004.10.360508
MA0006.10.210471
MA0007.10.346734
MA0009.10.780842
MA0014.10.00520703
MA0017.10.658116
MA0019.10.603066
MA0024.10.737933
MA0025.11.01089
MA0027.12.42079
MA0028.10.219287
MA0029.10.716673
MA0030.10.723093
MA0031.10.688336
MA0038.10.496338
MA0040.10.79313
MA0041.10.79301
MA0042.11.40102
MA0043.10.875991
MA0046.10.816137
MA0048.10.066679
MA0050.10.396459
MA0051.10.504875
MA0052.10.801048
MA0055.10.0660514
MA0056.10
MA0057.10.059732
MA0058.10.752621
MA0059.10.28489
MA0060.10.446031
MA0061.10.504772
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.10.0621035
MA0069.10.801381
MA0070.10.791856
MA0071.10.395679
MA0072.10.783532
MA0073.10.916511
MA0074.10.451832
MA0076.10.249619
MA0077.10.762273
MA0078.10.536502
MA0081.10.305576
MA0083.10.875209
MA0084.11.44691
MA0087.10.832758
MA0088.10.0379749
MA0089.10
MA0090.10.329158
MA0091.10.372635
MA0092.10.329444
MA0093.10.226349
MA0095.10
MA0098.10
MA0100.10.440912
MA0101.10.292867
MA0103.10.242398
MA0105.10.0911942
MA0106.10.543967
MA0107.10.66744
MA0108.20.625209
MA0109.10
MA0111.10.90605
MA0113.10.516916
MA0114.12.19906
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
MA0136.11.18666
MA0139.10.121562
MA0140.11.12231
MA0141.10.259554
MA0142.10.674191
MA0143.10.53259
MA0144.10.169559
MA0145.11.03071
MA0146.10.0389394
MA0147.10.179496
MA0148.10.375491
MA0149.10.2978
MA0062.20.0948004
MA0035.21.1319
MA0039.20.00879115
MA0138.21.44221
MA0002.20.781868
MA0137.20.257017
MA0104.20.134457
MA0047.20.495607
MA0112.20.0422488
MA0065.21.03323
MA0150.10.346631
MA0151.10
MA0152.10.495709
MA0153.10.92832
MA0154.10.0653255
MA0155.10.0498353
MA0156.10.694831
MA0157.10.642984
MA0158.10
MA0159.10.187774
MA0160.10.378276
MA0161.10
MA0162.10.00972009
MA0163.10.00834216
MA0164.10.471016
MA0080.20.237846
MA0018.20.480226
MA0099.20.584892
MA0079.25.7756e-05
MA0102.21.49914
MA0258.10.156336
MA0259.10.170828
MA0442.10
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