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MCL coexpression mm9:635: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000160!3.00e-11!31;UBERON:0000344!2.83e-08!15;UBERON:0001242!3.86e-07!13;UBERON:0000060!3.86e-07!13;UBERON:0001262!3.86e-07!13;UBERON:0004786!3.86e-07!13;UBERON:0007100!7.28e-07!18;UBERON:0000948!7.28e-07!18;UBERON:0005498!7.28e-07!18;UBERON:0004140!7.28e-07!18;UBERON:0009881!7.28e-07!18;UBERON:0004141!7.28e-07!18;UBERON:0003084!7.28e-07!18;UBERON:0007005!7.28e-07!18;UBERON:0004139!7.28e-07!18;UBERON:0004291!7.28e-07!18
|ontology_enrichment_uberon=UBERON:0000160!3.00e-11!31;UBERON:0000344!2.83e-08!15;UBERON:0001242!3.86e-07!13;UBERON:0000060!3.86e-07!13;UBERON:0001262!3.86e-07!13;UBERON:0004786!3.86e-07!13;UBERON:0007100!7.28e-07!18;UBERON:0000948!7.28e-07!18;UBERON:0005498!7.28e-07!18;UBERON:0004140!7.28e-07!18;UBERON:0009881!7.28e-07!18;UBERON:0004141!7.28e-07!18;UBERON:0003084!7.28e-07!18;UBERON:0007005!7.28e-07!18;UBERON:0004139!7.28e-07!18;UBERON:0004291!7.28e-07!18
|tfbs_overrepresentation_for_novel_motifs=0.795069,0.490989,0.269904,1.58049,0.176699,0.342839,0.425757,0.345089,0.112618,2.24671,0.385334,0.414631,0.106288,0.437133,0.189961,0,0.619876,0.170475,0.096222,1.06389,0.238546,1.20521,0.436294,0.520732,0.758244,2.03716,0.630402,0.361771,0.213277,1.29897,0.349031,0.717576,0.168723,0.570676,0.556756,0.308746,0.161521,0.411296,0.144953,0.391645,0.173534,0.353696,0.255102,0.191571,1.11259,0.856658,1.34233,1.74231,0.208261,0.215702,0.603113,0.488021,0.0612063,0.855661,0.87275,0.443782,0.223087,0.40287,0.60268,0.441884,0.698157,0.496904,0.383763,0.592318,5.19903,0.631188,1.00675,1.3527,0.693631,1.20659,0.253722,0.110167,0.299271,0.905636,0.0810502,0.54852,0.0786324,0.532872,1.63162,0.679143,0.110993,0.636582,0.495545,0.101814,0.792744,0.444993,0.4982,0.0651072,4.58964,1.51408,1.07554,0.797601,0.730003,0.181374,0.141946,0.129056,0.340672,0.732731,1.34284,0.0534645,0.486605,0.717305,0.838603,0.603683,0.602672,0.353298,0.660145,0.372438,8.78026,0.67437,0.286453,0.840348,0.243062,0.390066,1.0825,0.172131,0.337757,0.333247,0.621127,0.158673,0.910937,0.572279,0.464505,0.532013,1.13603,0.685116,0.433317,0.723425,1.00525,1.03388,0.821997,7.52951,0.976125,0.456508,1.10385,0.115066,0.300001,0.35497,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.354106,0.546641,1.84176,0.302077,1.60254,1.8264,0.103135,0.857198,0.133365,0.455644,0.93735,0.488969,0.199652,0.290467,0.299755,1.06466,0.791909,1.63996,0.284483,0.593295,0.448733,1.50123,0.413167,0.935682
|tfbs_overrepresentation_for_novel_motifs=0.795069,0.490989,0.269904,1.58049,0.176699,0.342839,0.425757,0.345089,0.112618,2.24671,0.385334,0.414631,0.106288,0.437133,0.189961,0,0.619876,0.170475,0.096222,1.06389,0.238546,1.20521,0.436294,0.520732,0.758244,2.03716,0.630402,0.361771,0.213277,1.29897,0.349031,0.717576,0.168723,0.570676,0.556756,0.308746,0.161521,0.411296,0.144953,0.391645,0.173534,0.353696,0.255102,0.191571,1.11259,0.856658,1.34233,1.74231,0.208261,0.215702,0.603113,0.488021,0.0612063,0.855661,0.87275,0.443782,0.223087,0.40287,0.60268,0.441884,0.698157,0.496904,0.383763,0.592318,5.19903,0.631188,1.00675,1.3527,0.693631,1.20659,0.253722,0.110167,0.299271,0.905636,0.0810502,0.54852,0.0786324,0.532872,1.63162,0.679143,0.110993,0.636582,0.495545,0.101814,0.792744,0.444993,0.4982,0.0651072,4.58964,1.51408,1.07554,0.797601,0.730003,0.181374,0.141946,0.129056,0.340672,0.732731,1.34284,0.0534645,0.486605,0.717305,0.838603,0.603683,0.602672,0.353298,0.660145,0.372438,8.78026,0.67437,0.286453,0.840348,0.243062,0.390066,1.0825,0.172131,0.337757,0.333247,0.621127,0.158673,0.910937,0.572279,0.464505,0.532013,1.13603,0.685116,0.433317,0.723425,1.00525,1.03388,0.821997,7.52951,0.976125,0.456508,1.10385,0.115066,0.300001,0.35497,1.05527,1.88134,1.48237,1.01139,0.475785,0.727736,0.596462,0.354106,0.546641,1.84176,0.302077,1.60254,1.8264,0.103135,0.857198,0.133365,0.455644,0.93735,0.488969,0.199652,0.290467,0.299755,1.06466,0.791909,1.63996,0.284483,0.593295,0.448733,1.50123,0.413167,0.935682
|tfbs_overrepresentation_jaspar=MA0003.1;0.0832519,MA0004.1;0.330313,MA0006.1;0.547312,MA0007.1;0.316976,MA0009.1;0.743257,MA0014.1;0.919317,MA0017.1;0.598706,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;0.054097,MA0050.1;0.365212,MA0051.1;0.471092,MA0052.1;0.76328,MA0055.1;0.0494654,MA0056.1;0,MA0057.1;0.71676,MA0058.1;0.246908,MA0059.1;0.257372,MA0060.1;0.395347,MA0061.1;0.147394,MA0063.1;0,MA0066.1;0.452472,MA0067.1;1.08124,MA0068.1;0.0500842,MA0069.1;0.76361,MA0070.1;0.75417,MA0071.1;0.364454,MA0072.1;0.745922,MA0073.1;0.000531005,MA0074.1;0.419185,MA0076.1;0.635923,MA0077.1;0.724865,MA0078.1;0.502121,MA0081.1;0.277253,MA0083.1;0.836845,MA0084.1;1.4063,MA0087.1;0.794721,MA0088.1;0.28966,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;0.0759118,MA0106.1;3.23418,MA0107.1;0.211681,MA0108.2;0.589413,MA0109.1;0,MA0111.1;0.839864,MA0113.1;0.482899,MA0114.1;2.0321,MA0115.1;0.84036,MA0116.1;0.186271,MA0117.1;0.808813,MA0119.1;1.34784,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;1.14144,MA0140.1;0.408417,MA0141.1;0.658164,MA0142.1;0.63775,MA0143.1;0.49828,MA0144.1;0.147954,MA0145.1;0.133285,MA0146.1;2.62666,MA0147.1;0.157258,MA0148.1;0.344843,MA0149.1;0.269772,MA0062.2;0.271822,MA0035.2;0.412747,MA0039.2;3.83682,MA0138.2;1.36778,MA0002.2;0.699393,MA0137.2;0.230686,MA0104.2;0.744492,MA0047.2;0.46201,MA0112.2;0.0329566,MA0065.2;1.30208,MA0150.1;0.316876,MA0151.1;0,MA0152.1;0.46211,MA0153.1;0.889592,MA0154.1;0.0529077,MA0155.1;0.637282,MA0156.1;0.222905,MA0157.1;0.606944,MA0158.1;0,MA0159.1;0.165031,MA0160.1;0.918217,MA0161.1;0,MA0162.1;0.103104,MA0163.1;0.0308606,MA0164.1;1.95358,MA0080.2;0.212408,MA0018.2;4.01071,MA0099.2;0.549696,MA0079.2;2.22608,MA0102.2;1.45844,MA0258.1;0.421574,MA0259.1;0.891672,MA0442.1;0
}}
}}

Revision as of 12:04, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:127774817..127774874,+p1@Cs
Mm9::chr11:6191663..6191690,+p2@Ogdh
Mm9::chr4:116230385..116230404,+p5@Gpbp1l1
Mm9::chr5:136254498..136254515,+p3@Mdh2
Mm9::chr5:136254517..136254533,+p1@Mdh2
Mm9::chr5:136254544..136254559,+p2@Mdh2
Mm9::chr5:136254570..136254582,+p4@Mdh2
Mm9::chr7:104727938..104728011,-p1@1810020D17Rik
Mm9::chr8:42101937..42101968,-p5@Mtus1
Mm9::chr9:108839183..108839195,-p@chr9:108839183..108839195
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Mm9::chr9:108839202..108839231,-p@chr9:108839202..108839231
-


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:0006096glycolysis0.000719686101583094
GO:0006007glucose catabolic process0.000719686101583094
GO:0046365monosaccharide catabolic process0.000719686101583094
GO:0019320hexose catabolic process0.000719686101583094
GO:0046164alcohol catabolic process0.000719686101583094
GO:0044275cellular carbohydrate catabolic process0.000835044202329801
GO:0016052carbohydrate catabolic process0.000852708932219754
GO:0006006glucose metabolic process0.00135788563649404
GO:0005739mitochondrion0.0017805292280721
GO:0019318hexose metabolic process0.0017805292280721
GO:0005996monosaccharide metabolic process0.0017805292280721
GO:0050164oxoglutarate dehydrogenase (NADP+) activity0.0017805292280721
GO:0004591oxoglutarate dehydrogenase (succinyl-transferring) activity0.00305216858660128
GO:0004691cAMP-dependent protein kinase activity0.00305216858660128
GO:0044265cellular macromolecule catabolic process0.00377011932676117
GO:0030976thiamin pyrophosphate binding0.00377011932676117
GO:0030060L-malate dehydrogenase activity0.00377011932676117
GO:0044262cellular carbohydrate metabolic process0.0039228738921035
GO:0006066alcohol metabolic process0.0039228738921035
GO:0004690cyclic nucleotide-dependent protein kinase activity0.0042725677946356
GO:0009057macromolecule catabolic process0.00468653004588212
GO:0006108malate metabolic process0.00485492465245523
GO:0005975carbohydrate metabolic process0.00603378529492736
GO:0016624oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor0.00622980388168085
GO:0016615malate dehydrogenase activity0.00683461031047704
GO:0044248cellular catabolic process0.00711899562963582
GO:0043648dicarboxylic acid metabolic process0.00711899562963582
GO:0031594neuromuscular junction0.00991357063876156
GO:0009056catabolic process0.0106749828994384
GO:0006100tricarboxylic acid cycle intermediate metabolic process0.0106749828994384
GO:0051969regulation of transmission of nerve impulse0.0133400725415185
GO:0050804regulation of synaptic transmission0.0133400725415185
GO:0006099tricarboxylic acid cycle0.0145990669148224
GO:0046356acetyl-CoA catabolic process0.0145990669148224
GO:0001707mesoderm formation0.0145990669148224
GO:0048332mesoderm morphogenesis0.0145990669148224
GO:0031644regulation of neurological process0.0145990669148224
GO:0009060aerobic respiration0.0145990669148224
GO:0001704formation of primary germ layer0.0147303354289522
GO:0044444cytoplasmic part0.0147303354289522
GO:0009109coenzyme catabolic process0.0147303354289522
GO:0016620oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor0.0147303354289522
GO:0045333cellular respiration0.0148060594833286
GO:0016491oxidoreductase activity0.0148060594833286
GO:0051187cofactor catabolic process0.0151680576498623
GO:0006084acetyl-CoA metabolic process0.0157639835889618
GO:0016903oxidoreductase activity, acting on the aldehyde or oxo group of donors0.0172399256059361
GO:0007498mesoderm development0.0217541713803542
GO:0007369gastrulation0.0269447198396174
GO:0015980energy derivation by oxidation of organic compounds0.0281032602653716
GO:0048729tissue morphogenesis0.0312938817120633
GO:0019842vitamin binding0.0428982228502034
GO:0016616oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor0.0440809510405541
GO:0050662coenzyme binding0.0456094997535444
GO:0016614oxidoreductase activity, acting on CH-OH group of donors0.0459307794156284



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
intestine3.00e-1131
mucosa2.83e-0815
intestinal mucosa3.86e-0713
anatomical wall3.86e-0713
wall of intestine3.86e-0713
gastrointestinal system mucosa3.86e-0713
primary circulatory organ7.28e-0718
heart7.28e-0718
primitive heart tube7.28e-0718
primary heart field7.28e-0718
anterior lateral plate mesoderm7.28e-0718
heart tube7.28e-0718
heart primordium7.28e-0718
cardiac mesoderm7.28e-0718
cardiogenic plate7.28e-0718
heart rudiment7.28e-0718


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)
MA0003.10.0832519
MA0004.10.330313
MA0006.10.547312
MA0007.10.316976
MA0009.10.743257
MA0014.10.919317
MA0017.10.598706
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
MA0048.10.054097
MA0050.10.365212
MA0051.10.471092
MA0052.10.76328
MA0055.10.0494654
MA0056.10
MA0057.10.71676
MA0058.10.246908
MA0059.10.257372
MA0060.10.395347
MA0061.10.147394
MA0063.10
MA0066.10.452472
MA0067.11.08124
MA0068.10.0500842
MA0069.10.76361
MA0070.10.75417
MA0071.10.364454
MA0072.10.745922
MA0073.10.000531005
MA0074.10.419185
MA0076.10.635923
MA0077.10.724865
MA0078.10.502121
MA0081.10.277253
MA0083.10.836845
MA0084.11.4063
MA0087.10.794721
MA0088.10.28966
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
MA0105.10.0759118
MA0106.13.23418
MA0107.10.211681
MA0108.20.589413
MA0109.10
MA0111.10.839864
MA0113.10.482899
MA0114.12.0321
MA0115.10.84036
MA0116.10.186271
MA0117.10.808813
MA0119.11.34784
MA0122.10.828211
MA0124.11.02871
MA0125.10.955734
MA0130.10
MA0131.10.563262
MA0132.10
MA0133.10
MA0135.10.873285
MA0136.10.437601
MA0139.11.14144
MA0140.10.408417
MA0141.10.658164
MA0142.10.63775
MA0143.10.49828
MA0144.10.147954
MA0145.10.133285
MA0146.12.62666
MA0147.10.157258
MA0148.10.344843
MA0149.10.269772
MA0062.20.271822
MA0035.20.412747
MA0039.23.83682
MA0138.21.36778
MA0002.20.699393
MA0137.20.230686
MA0104.20.744492
MA0047.20.46201
MA0112.20.0329566
MA0065.21.30208
MA0150.10.316876
MA0151.10
MA0152.10.46211
MA0153.10.889592
MA0154.10.0529077
MA0155.10.637282
MA0156.10.222905
MA0157.10.606944
MA0158.10
MA0159.10.165031
MA0160.10.918217
MA0161.10
MA0162.10.103104
MA0163.10.0308606
MA0164.11.95358
MA0080.20.212408
MA0018.24.01071
MA0099.20.549696
MA0079.22.22608
MA0102.21.45844
MA0258.10.421574
MA0259.10.891672
MA0442.10
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