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MCL coexpression mm9:646: Difference between revisions

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{{MCL_coexpression_mm9
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3-dioxygenase activity;2.7414764005448e-05;14789,56401!GO:0031544;peptidyl-proline 3-dioxygenase activity;2.7414764005448e-05;14789,56401!GO:0031543;peptidyl-proline dioxygenase activity;6.84993630874524e-05;14789,56401!GO:0019798;procollagen-proline dioxygenase activity;6.84993630874524e-05;14789,56401!GO:0031418;L-ascorbic acid binding;0.000623232287222115;14789,56401!GO:0016706;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors;0.000910159940640849;14789,56401!GO:0051213;dioxygenase activity;0.00355713241597084;14789,56401!GO:0016702;oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen;0.00355713241597084;14789,56401!GO:0016701;oxidoreductase activity, acting on single donors with incorporation of molecular oxygen;0.00355713241597084;14789,56401!GO:0019842;vitamin binding;0.00979460778428785;14789,56401!GO:0016705;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen;0.0125925493366994;14789,56401!GO:0005783;endoplasmic reticulum;0.0192911193069523;52377,14789,56401!GO:0005578;proteinaceous extracellular matrix;0.0497556147605712;56401,56693!GO:0042733;embryonic digit morphogenesis;0.0497556147605712;14673!GO:0005506;iron ion 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|gostat_on_MCL_coexpression=GO:0019797;procollagen-proline 3-dioxygenase activity;2.7414764005448e-05;14789,56401!GO:0031544;peptidyl-proline 3-dioxygenase activity;2.7414764005448e-05;14789,56401!GO:0031543;peptidyl-proline dioxygenase activity;6.84993630874524e-05;14789,56401!GO:0019798;procollagen-proline dioxygenase activity;6.84993630874524e-05;14789,56401!GO:0031418;L-ascorbic acid binding;0.000623232287222115;14789,56401!GO:0016706;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors;0.000910159940640849;14789,56401!GO:0051213;dioxygenase activity;0.00355713241597084;14789,56401!GO:0016702;oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen;0.00355713241597084;14789,56401!GO:0016701;oxidoreductase activity, acting on single donors with incorporation of molecular oxygen;0.00355713241597084;14789,56401!GO:0019842;vitamin binding;0.00979460778428785;14789,56401!GO:0016705;oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen;0.0125925493366994;14789,56401!GO:0005783;endoplasmic reticulum;0.0192911193069523;52377,14789,56401!GO:0005578;proteinaceous extracellular matrix;0.0497556147605712;56401,56693!GO:0042733;embryonic digit morphogenesis;0.0497556147605712;14673!GO:0005506;iron ion binding;0.0497556147605712;14789,56401!
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=
|tfbs_overrepresentation_for_novel_motifs=0.29262,0.140695,0.7433,0.329881,0.176699,0.342839,0.425757,0.345089,0.362206,0.660314,0.385334,0.414631,0.703175,0.437133,0.189961,0,0.619876,0.170475,0.096222,0.387499,0.670854,0.831639,0.436294,0.520732,0.276437,0.4628,0.304017,0.949712,0.611503,0.500344,0.349031,0.717576,1.54849,0.570676,0.556756,1.69598,0.161521,1.0583,0.445168,1.85421,0.173534,0.353696,0.255102,0.559697,1.11259,0.856658,0.543674,0.376103,0.081888,0.215702,0.603113,0.488021,0.829247,0.855661,0.87275,0.443782,0.223087,0.40287,0.288386,0.441884,0.698157,0.496904,0.383763,0.592318,0.45416,0.631188,1.00675,1.3527,0.693631,1.20659,0.706068,0.355763,0.126035,0.905636,0.277092,0.258161,0.0786324,0.532872,0.681539,0.242107,0.110993,0.636582,1.23994,0.333618,0.792744,0.123451,0.143445,2.37644,0.548334,1.51408,1.07554,0.797601,0.730003,0.181374,0.141946,0.404817,0.694736,0.732731,0.543917,0.437273,1.50667,0.717305,0.838603,0.603683,0.602672,0.930972,0.660145,0.372438,0.246223,0.240055,0.286453,0.840348,0.681364,0.390066,1.0825,0.512539,0.566805,0.333247,0.621127,0.158673,0.910937,0.572279,0.464505,0.532013,1.13603,0.685116,1.10612,0.723425,1.00525,0.540802,0.821997,0.864341,0.976125,1.1562,1.10385,0.0275241,0.300001,0.35497,1.05527,1.88134,1.48237,1.01139,2.08054,0.727736,0.596462,0.354106,0.546641,1.84176,0.302077,0.178088,0.507931,0.252821,0.857198,0.133365,0.455644,0.93735,0.488969,0.57908,0.290467,0.811219,1.06466,0.791909,0.685546,0.284483,0.593295,0.448733,0.939822,1.86958,2.37988
|tfbs_overrepresentation_jaspar=MA0003.1;1.90003,MA0004.1;0.330313,MA0006.1;0.186435,MA0007.1;0.316976,MA0009.1;0.743257,MA0014.1;1.22114,MA0017.1;0.207884,MA0019.1;0.567591,MA0024.1;0.70077,MA0025.1;0.971686,MA0027.1;2.37948,MA0028.1;0.567414,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;0.252679,MA0043.1;0.837621,MA0046.1;0.778239,MA0048.1;0.769903,MA0050.1;0.365212,MA0051.1;0.471092,MA0052.1;0.76328,MA0055.1;0.735247,MA0056.1;0,MA0057.1;1.10344,MA0058.1;0.246908,MA0059.1;0.257372,MA0060.1;1.28515,MA0061.1;0.147394,MA0063.1;0,MA0066.1;0.452472,MA0067.1;1.08124,MA0068.1;0.187364,MA0069.1;0.76361,MA0070.1;0.75417,MA0071.1;0.364454,MA0072.1;0.745922,MA0073.1;1.18906,MA0074.1;0.419185,MA0076.1;0.223625,MA0077.1;0.724865,MA0078.1;0.502121,MA0081.1;0.760108,MA0083.1;0.836845,MA0084.1;1.4063,MA0087.1;0.794721,MA0088.1;1.22895,MA0089.1;0,MA0090.1;0.299987,MA0091.1;0.342071,MA0092.1;0.300264,MA0093.1;0.20148,MA0095.1;0,MA0098.1;0,MA0100.1;0.408523,MA0101.1;0.265031,MA0103.1;0.216742,MA0105.1;0.556739,MA0106.1;0.509454,MA0107.1;0.211681,MA0108.2;0.589413,MA0109.1;0,MA0111.1;0.839864,MA0113.1;0.482899,MA0114.1;0.145642,MA0115.1;0.84036,MA0116.1;0.546914,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;0.338099,MA0140.1;0.408417,MA0141.1;0.233109,MA0142.1;0.63775,MA0143.1;0.49828,MA0144.1;0.147954,MA0145.1;0.0329586,MA0146.1;0.775515,MA0147.1;0.157258,MA0148.1;0.344843,MA0149.1;0.742998,MA0062.2;0.271822,MA0035.2;0.412747,MA0039.2;1.96175,MA0138.2;0.555696,MA0002.2;0.105469,MA0137.2;0.230686,MA0104.2;0.369356,MA0047.2;0.46201,MA0112.2;0.0329566,MA0065.2;0.314773,MA0150.1;0.849777,MA0151.1;0,MA0152.1;0.46211,MA0153.1;0.889592,MA0154.1;2.16263,MA0155.1;1.89657,MA0156.1;0.222905,MA0157.1;0.606944,MA0158.1;0,MA0159.1;0.495113,MA0160.1;0.347545,MA0161.1;0,MA0162.1;0.388731,MA0163.1;2.27461,MA0164.1;0.437937,MA0080.2;0.212408,MA0018.2;0.446948,MA0099.2;0.549696,MA0079.2;2.96303,MA0102.2;1.45844,MA0258.1;0.421574,MA0259.1;0.455671,MA0442.1;0
}}

Latest revision as of 15:39, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:102017653..102017728,-p1@Tmem101
Mm9::chr4:118905501..118905561,+p1@Lepre1
Mm9::chr5:141306409..141306421,-p4@Gna12
Mm9::chr6:124807158..124807183,+p@chr6:124807158..124807183
+
Mm9::chr6:124807705..124807723,-p2@Leprel2
Mm9::chr6:124807725..124807773,-p1@Leprel2
Mm9::chr7:52124998..52125094,-p1@Ptov1
Mm9::chr7:52347053..52347075,-p4@Rcn3
Mm9::chr7:52347083..52347104,-p2@Rcn3
Mm9::chr7:52347500..52347551,-p1@Rcn3
Mm9::chr9:114299751..114299805,-p1@Crtap


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:0019797procollagen-proline 3-dioxygenase activity2.7414764005448e-05
GO:0031544peptidyl-proline 3-dioxygenase activity2.7414764005448e-05
GO:0031543peptidyl-proline dioxygenase activity6.84993630874524e-05
GO:0019798procollagen-proline dioxygenase activity6.84993630874524e-05
GO:0031418L-ascorbic acid binding0.000623232287222115
GO:0016706oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors0.000910159940640849
GO:0051213dioxygenase activity0.00355713241597084
GO:0016702oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen0.00355713241597084
GO:0016701oxidoreductase activity, acting on single donors with incorporation of molecular oxygen0.00355713241597084
GO:0019842vitamin binding0.00979460778428785
GO:0016705oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen0.0125925493366994
GO:0005783endoplasmic reticulum0.0192911193069523
GO:0005578proteinaceous extracellular matrix0.0497556147605712
GO:0042733embryonic digit morphogenesis0.0497556147605712
GO:0005506iron ion binding0.0497556147605712



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><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)
MA0003.11.90003
MA0004.10.330313
MA0006.10.186435
MA0007.10.316976
MA0009.10.743257
MA0014.11.22114
MA0017.10.207884
MA0019.10.567591
MA0024.10.70077
MA0025.10.971686
MA0027.12.37948
MA0028.10.567414
MA0029.10.679737
MA0030.10.686088
MA0031.10.651724
MA0038.10.462726
MA0040.10.755433
MA0041.10.263922
MA0042.10.252679
MA0043.10.837621
MA0046.10.778239
MA0048.10.769903
MA0050.10.365212
MA0051.10.471092
MA0052.10.76328
MA0055.10.735247
MA0056.10
MA0057.11.10344
MA0058.10.246908
MA0059.10.257372
MA0060.11.28515
MA0061.10.147394
MA0063.10
MA0066.10.452472
MA0067.11.08124
MA0068.10.187364
MA0069.10.76361
MA0070.10.75417
MA0071.10.364454
MA0072.10.745922
MA0073.11.18906
MA0074.10.419185
MA0076.10.223625
MA0077.10.724865
MA0078.10.502121
MA0081.10.760108
MA0083.10.836845
MA0084.11.4063
MA0087.10.794721
MA0088.11.22895
MA0089.10
MA0090.10.299987
MA0091.10.342071
MA0092.10.300264
MA0093.10.20148
MA0095.10
MA0098.10
MA0100.10.408523
MA0101.10.265031
MA0103.10.216742
MA0105.10.556739
MA0106.10.509454
MA0107.10.211681
MA0108.20.589413
MA0109.10
MA0111.10.839864
MA0113.10.482899
MA0114.10.145642
MA0115.10.84036
MA0116.10.546914
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
MA0139.10.338099
MA0140.10.408417
MA0141.10.233109
MA0142.10.63775
MA0143.10.49828
MA0144.10.147954
MA0145.10.0329586
MA0146.10.775515
MA0147.10.157258
MA0148.10.344843
MA0149.10.742998
MA0062.20.271822
MA0035.20.412747
MA0039.21.96175
MA0138.20.555696
MA0002.20.105469
MA0137.20.230686
MA0104.20.369356
MA0047.20.46201
MA0112.20.0329566
MA0065.20.314773
MA0150.10.849777
MA0151.10
MA0152.10.46211
MA0153.10.889592
MA0154.12.16263
MA0155.11.89657
MA0156.10.222905
MA0157.10.606944
MA0158.10
MA0159.10.495113
MA0160.10.347545
MA0161.10
MA0162.10.388731
MA0163.12.27461
MA0164.10.437937
MA0080.20.212408
MA0018.20.446948
MA0099.20.549696
MA0079.22.96303
MA0102.21.45844
MA0258.10.421574
MA0259.10.455671
MA0442.10
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