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MCL coexpression mm9:674: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002107!3.71e-27!22;UBERON:0007499!3.71e-27!22;UBERON:0006925!3.71e-27!22;UBERON:0009497!3.71e-27!22;UBERON:0000015!3.71e-27!22;UBERON:0002423!3.71e-27!22;UBERON:0006235!3.71e-27!22;UBERON:0008835!3.71e-27!22;UBERON:0003894!3.71e-27!22;UBERON:0004161!3.71e-27!22;UBERON:0008836!3.71e-27!22;UBERON:0009854!1.15e-25!23;UBERON:0009856!1.15e-25!23;UBERON:0002365!4.83e-23!25;UBERON:0002330!4.83e-23!25;UBERON:0005172!2.33e-13!49;UBERON:0005173!2.33e-13!49;UBERON:0002417!2.33e-13!49;UBERON:0000916!2.33e-13!49;UBERON:0005256!4.90e-13!45;UBERON:0003104!2.98e-09!61;UBERON:0009142!2.98e-09!61;UBERON:0003914!3.71e-09!47;UBERON:0002368!4.92e-08!60;UBERON:0009569!5.20e-08!66;UBERON:0003929!5.81e-07!55;UBERON:0002530!6.44e-07!65;UBERON:0000949!7.35e-07!72;UBERON:0005177!9.32e-07!79
|ontology_enrichment_uberon=UBERON:0002107!3.71e-27!22;UBERON:0007499!3.71e-27!22;UBERON:0006925!3.71e-27!22;UBERON:0009497!3.71e-27!22;UBERON:0000015!3.71e-27!22;UBERON:0002423!3.71e-27!22;UBERON:0006235!3.71e-27!22;UBERON:0008835!3.71e-27!22;UBERON:0003894!3.71e-27!22;UBERON:0004161!3.71e-27!22;UBERON:0008836!3.71e-27!22;UBERON:0009854!1.15e-25!23;UBERON:0009856!1.15e-25!23;UBERON:0002365!4.83e-23!25;UBERON:0002330!4.83e-23!25;UBERON:0005172!2.33e-13!49;UBERON:0005173!2.33e-13!49;UBERON:0002417!2.33e-13!49;UBERON:0000916!2.33e-13!49;UBERON:0005256!4.90e-13!45;UBERON:0003104!2.98e-09!61;UBERON:0009142!2.98e-09!61;UBERON:0003914!3.71e-09!47;UBERON:0002368!4.92e-08!60;UBERON:0009569!5.20e-08!66;UBERON:0003929!5.81e-07!55;UBERON:0002530!6.44e-07!65;UBERON:0000949!7.35e-07!72;UBERON:0005177!9.32e-07!79
|tfbs_overrepresentation_for_novel_motifs=0.29262,0.0103138,0.269904,1.58049,0.52369,0.342839,0.425757,0.702429,0.112618,0.208174,0.385334,0.414631,0.106288,0.437133,0.189961,0,0.619876,0.508485,0.096222,0.171249,0.238546,0.117252,0.436294,0.520732,0.276437,0.4628,0.304017,0.361771,0.213277,0.500344,0.349031,0.717576,0.504188,0.270473,0.19035,0.075793,0.161521,0.411296,0.873942,0.123934,0.992655,0.353696,2.50731,1.67896,0.00546478,0.319944,0.543674,0.376103,1.35339,0.215702,0.603113,0.488021,0.220536,0.855661,0.87275,0.443782,0.223087,0.40287,0.0851299,0.441884,0.698157,0.496904,0.120887,0.592318,0.45416,0.631188,1.00675,1.3527,0.693631,1.20659,0.253722,0.720972,0.0307733,0.905636,0.0810502,0.0742951,0.0786324,0.532872,0.681539,0.242107,1.74285,0.636582,0.495545,0.101814,0.792744,0.00855221,0.0106044,0.0651072,1.3522,1.51408,1.07554,0.797601,0.730003,0.535058,0.141946,0.805383,0.694736,0.732731,0.543917,0.0534645,0.161581,0.717305,0.838603,0.603683,0.602672,0.353298,0.660145,0.372438,0.246223,0.240055,0.781068,0.840348,0.243062,0.390066,1.0825,0.172131,0.0135638,0.333247,0.621127,0.931584,0.910937,0.572279,0.464505,1.3176,1.13603,0.685116,0.433317,0.723425,1.00525,0.183744,0.821997,0.323373,0.976125,0.456508,1.10385,1.19208,0.811774,0.35497,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.354106,0.546641,1.84176,0.302077,0.178088,0.0664621,0.0240729,0.857198,0.133365,0.455644,6.67838,0.488969,0.199652,0.790184,0.299755,1.06466,0.791909,0.685546,0.284483,0.593295,0.448733,0.484323,0.413167,0.00349204
|tfbs_overrepresentation_for_novel_motifs=0.29262,0.0103138,0.269904,1.58049,0.52369,0.342839,0.425757,0.702429,0.112618,0.208174,0.385334,0.414631,0.106288,0.437133,0.189961,0,0.619876,0.508485,0.096222,0.171249,0.238546,0.117252,0.436294,0.520732,0.276437,0.4628,0.304017,0.361771,0.213277,0.500344,0.349031,0.717576,0.504188,0.270473,0.19035,0.075793,0.161521,0.411296,0.873942,0.123934,0.992655,0.353696,2.50731,1.67896,0.00546478,0.319944,0.543674,0.376103,1.35339,0.215702,0.603113,0.488021,0.220536,0.855661,0.87275,0.443782,0.223087,0.40287,0.0851299,0.441884,0.698157,0.496904,0.120887,0.592318,0.45416,0.631188,1.00675,1.3527,0.693631,1.20659,0.253722,0.720972,0.0307733,0.905636,0.0810502,0.0742951,0.0786324,0.532872,0.681539,0.242107,1.74285,0.636582,0.495545,0.101814,0.792744,0.00855221,0.0106044,0.0651072,1.3522,1.51408,1.07554,0.797601,0.730003,0.535058,0.141946,0.805383,0.694736,0.732731,0.543917,0.0534645,0.161581,0.717305,0.838603,0.603683,0.602672,0.353298,0.660145,0.372438,0.246223,0.240055,0.781068,0.840348,0.243062,0.390066,1.0825,0.172131,0.0135638,0.333247,0.621127,0.931584,0.910937,0.572279,0.464505,1.3176,1.13603,0.685116,0.433317,0.723425,1.00525,0.183744,0.821997,0.323373,0.976125,0.456508,1.10385,1.19208,0.811774,0.35497,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.354106,0.546641,1.84176,0.302077,0.178088,0.0664621,0.0240729,0.857198,0.133365,0.455644,6.67838,0.488969,0.199652,0.790184,0.299755,1.06466,0.791909,0.685546,0.284483,0.593295,0.448733,0.484323,0.413167,0.00349204
|tfbs_overrepresentation_jaspar=MA0003.1;0.000402533,MA0004.1;0.330313,MA0006.1;0.186435,MA0007.1;0.316976,MA0009.1;0.743257,MA0014.1;0.00333639,MA0017.1;0.207884,MA0019.1;0.567591,MA0024.1;0.70077,MA0025.1;0.971686,MA0027.1;2.37948,MA0028.1;0.194782,MA0029.1;0.679737,MA0030.1;0.686088,MA0031.1;0.651724,MA0038.1;0.462726,MA0040.1;0.755433,MA0041.1;0.263922,MA0042.1;0.703657,MA0043.1;0.837621,MA0046.1;4.40038,MA0048.1;2.18444,MA0050.1;0.365212,MA0051.1;0.471092,MA0052.1;0.76328,MA0055.1;4.35359,MA0056.1;0,MA0057.1;0.048013,MA0058.1;0.246908,MA0059.1;0.257372,MA0060.1;0.12537,MA0061.1;0.147394,MA0063.1;0,MA0066.1;0.452472,MA0067.1;1.08124,MA0068.1;0.735122,MA0069.1;0.76361,MA0070.1;0.75417,MA0071.1;2.56438,MA0072.1;7.15286,MA0073.1;2.58254e-05,MA0074.1;3.84778,MA0076.1;0.223625,MA0077.1;1.72158,MA0078.1;2.16799,MA0081.1;0.277253,MA0083.1;0.836845,MA0084.1;1.4063,MA0087.1;0.794721,MA0088.1;0.534411,MA0089.1;0,MA0090.1;0.299987,MA0091.1;0.906056,MA0092.1;0.300264,MA0093.1;0.20148,MA0095.1;0,MA0098.1;0,MA0100.1;1.05226,MA0101.1;0.265031,MA0103.1;0.216742,MA0105.1;0.0759118,MA0106.1;0.509454,MA0107.1;0.211681,MA0108.2;0.589413,MA0109.1;0,MA0111.1;2.31164,MA0113.1;0.482899,MA0114.1;0.145642,MA0115.1;0.84036,MA0116.1;0.186271,MA0117.1;0.808813,MA0119.1;0.265536,MA0122.1;0.828211,MA0124.1;1.02871,MA0125.1;0.955734,MA0130.1;0,MA0131.1;0.563262,MA0132.1;0,MA0133.1;0,MA0135.1;0.873285,MA0136.1;0.437601,MA0139.1;0.103495,MA0140.1;0.408417,MA0141.1;0.233109,MA0142.1;0.63775,MA0143.1;3.18395,MA0144.1;2.74889,MA0145.1;0.133285,MA0146.1;0.0276106,MA0147.1;0.157258,MA0148.1;0.344843,MA0149.1;0.269772,MA0062.2;0.0791588,MA0035.2;0.412747,MA0039.2;0.0156442,MA0138.2;1.36778,MA0002.2;0.343346,MA0137.2;4.40331,MA0104.2;0.11535,MA0047.2;0.46201,MA0112.2;0.0329566,MA0065.2;0.314773,MA0150.1;0.316876,MA0151.1;0,MA0152.1;0.46211,MA0153.1;3.40284,MA0154.1;0.195907,MA0155.1;0.0394399,MA0156.1;0.222905,MA0157.1;0.606944,MA0158.1;0,MA0159.1;0.165031,MA0160.1;0.347545,MA0161.1;0,MA0162.1;0.00661648,MA0163.1;0.0308606,MA0164.1;0.437937,MA0080.2;0.212408,MA0018.2;0.446948,MA0099.2;0.549696,MA0079.2;1.32826e-05,MA0102.2;1.45844,MA0258.1;0.135621,MA0259.1;0.14914,MA0442.1;0
}}
}}

Revision as of 12:08, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr15:89165417..89165448,+p2@Miox
Mm9::chr16:22899188..22899189,-p@chr16:22899188..22899189
-
Mm9::chr1:174825056..174825089,-p1@Apcs
Mm9::chr1:174825099..174825111,-p6@Apcs
Mm9::chr1:174825114..174825134,-p4@Apcs
Mm9::chr1:174825139..174825146,-p5@Apcs
Mm9::chr1:174825156..174825175,-p3@Apcs
Mm9::chr3:82846342..82846366,+p@chr3:82846342..82846366
+
Mm9::chr3:82847141..82847172,+p@chr3:82847141..82847172
+
Mm9::chr7:107699259..107699268,-p@chr7:107699259..107699268
-
Mm9::chr8:23674552..23674588,+p@chr8:23674552..23674588
+


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:0050113inositol oxygenase activity0.00219142058839643
GO:0004033aldo-keto reductase activity0.0164293510171321
GO:0016701oxidoreductase activity, acting on single donors with incorporation of molecular oxygen0.0360940550224503
GO:0016651oxidoreductase activity, acting on NADH or NADPH0.0360940550224503
GO:0016616oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor0.0433226793136719
GO:0016614oxidoreductase activity, acting on CH-OH group of donors0.0433226793136719



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
liver3.71e-2722
epithelial sac3.71e-2722
digestive gland3.71e-2722
epithelium of foregut-midgut junction3.71e-2722
anatomical boundary3.71e-2722
hepatobiliary system3.71e-2722
foregut-midgut junction3.71e-2722
hepatic diverticulum3.71e-2722
liver primordium3.71e-2722
septum transversum3.71e-2722
liver bud3.71e-2722
digestive tract diverticulum1.15e-2523
sac1.15e-2523
exocrine gland4.83e-2325
exocrine system4.83e-2325
abdomen element2.33e-1349
abdominal segment element2.33e-1349
abdominal segment of trunk2.33e-1349
abdomen2.33e-1349
trunk mesenchyme4.90e-1345
mesenchyme2.98e-0961
entire embryonic mesenchyme2.98e-0961
epithelial tube3.71e-0947
endocrine gland4.92e-0860
subdivision of trunk5.20e-0866
gut epithelium5.81e-0755
gland6.44e-0765
endocrine system7.35e-0772
trunk region element9.32e-0779


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)
MA0003.10.000402533
MA0004.10.330313
MA0006.10.186435
MA0007.10.316976
MA0009.10.743257
MA0014.10.00333639
MA0017.10.207884
MA0019.10.567591
MA0024.10.70077
MA0025.10.971686
MA0027.12.37948
MA0028.10.194782
MA0029.10.679737
MA0030.10.686088
MA0031.10.651724
MA0038.10.462726
MA0040.10.755433
MA0041.10.263922
MA0042.10.703657
MA0043.10.837621
MA0046.14.40038
MA0048.12.18444
MA0050.10.365212
MA0051.10.471092
MA0052.10.76328
MA0055.14.35359
MA0056.10
MA0057.10.048013
MA0058.10.246908
MA0059.10.257372
MA0060.10.12537
MA0061.10.147394
MA0063.10
MA0066.10.452472
MA0067.11.08124
MA0068.10.735122
MA0069.10.76361
MA0070.10.75417
MA0071.12.56438
MA0072.17.15286
MA0073.12.58254e-05
MA0074.13.84778
MA0076.10.223625
MA0077.11.72158
MA0078.12.16799
MA0081.10.277253
MA0083.10.836845
MA0084.11.4063
MA0087.10.794721
MA0088.10.534411
MA0089.10
MA0090.10.299987
MA0091.10.906056
MA0092.10.300264
MA0093.10.20148
MA0095.10
MA0098.10
MA0100.11.05226
MA0101.10.265031
MA0103.10.216742
MA0105.10.0759118
MA0106.10.509454
MA0107.10.211681
MA0108.20.589413
MA0109.10
MA0111.12.31164
MA0113.10.482899
MA0114.10.145642
MA0115.10.84036
MA0116.10.186271
MA0117.10.808813
MA0119.10.265536
MA0122.10.828211
MA0124.11.02871
MA0125.10.955734
MA0130.10
MA0131.10.563262
MA0132.10
MA0133.10
MA0135.10.873285
MA0136.10.437601
MA0139.10.103495
MA0140.10.408417
MA0141.10.233109
MA0142.10.63775
MA0143.13.18395
MA0144.12.74889
MA0145.10.133285
MA0146.10.0276106
MA0147.10.157258
MA0148.10.344843
MA0149.10.269772
MA0062.20.0791588
MA0035.20.412747
MA0039.20.0156442
MA0138.21.36778
MA0002.20.343346
MA0137.24.40331
MA0104.20.11535
MA0047.20.46201
MA0112.20.0329566
MA0065.20.314773
MA0150.10.316876
MA0151.10
MA0152.10.46211
MA0153.13.40284
MA0154.10.195907
MA0155.10.0394399
MA0156.10.222905
MA0157.10.606944
MA0158.10
MA0159.10.165031
MA0160.10.347545
MA0161.10
MA0162.10.00661648
MA0163.10.0308606
MA0164.10.437937
MA0080.20.212408
MA0018.20.446948
MA0099.20.549696
MA0079.21.32826e-05
MA0102.21.45844
MA0258.10.135621
MA0259.10.14914
MA0442.10
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