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MCL coexpression mm9:1180: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002323!4.99e-20!37;UBERON:0004458!4.99e-20!37;UBERON:0003886!4.32e-19!38;UBERON:0002553!3.31e-18!39;UBERON:0005156!2.03e-17!26;UBERON:0000990!2.03e-17!26;UBERON:0003133!1.57e-16!24;UBERON:0000991!3.48e-14!18;UBERON:0005564!3.48e-14!18;UBERON:0004176!2.56e-13!17;UBERON:0009196!2.56e-13!17;UBERON:0009117!2.56e-13!17;UBERON:0000464!1.09e-11!57;UBERON:0000473!9.71e-11!14;UBERON:0001008!2.65e-10!19;UBERON:0004872!4.35e-10!33;UBERON:0006554!6.99e-10!18;UBERON:0003101!1.26e-09!16;UBERON:0000079!1.26e-09!16;UBERON:0003135!1.28e-09!15;UBERON:0003103!2.76e-09!43;UBERON:0002113!1.89e-08!14;UBERON:0003918!1.89e-08!14;UBERON:0011143!1.89e-08!14;UBERON:0005095!1.89e-08!14;UBERON:0007687!1.89e-08!14;UBERON:0000474!2.47e-08!9;UBERON:0000466!5.49e-08!79;UBERON:0007100!1.24e-07!18;UBERON:0000948!1.24e-07!18;UBERON:0005498!1.24e-07!18;UBERON:0004140!1.24e-07!18;UBERON:0009881!1.24e-07!18;UBERON:0004141!1.24e-07!18;UBERON:0003084!1.24e-07!18;UBERON:0007005!1.24e-07!18;UBERON:0004139!1.24e-07!18;UBERON:0004291!1.24e-07!18;UBERON:0003134!1.88e-07!8;UBERON:0002075!1.97e-07!19;UBERON:0005177!3.08e-07!79
|ontology_enrichment_uberon=UBERON:0002323!4.99e-20!37;UBERON:0004458!4.99e-20!37;UBERON:0003886!4.32e-19!38;UBERON:0002553!3.31e-18!39;UBERON:0005156!2.03e-17!26;UBERON:0000990!2.03e-17!26;UBERON:0003133!1.57e-16!24;UBERON:0000991!3.48e-14!18;UBERON:0005564!3.48e-14!18;UBERON:0004176!2.56e-13!17;UBERON:0009196!2.56e-13!17;UBERON:0009117!2.56e-13!17;UBERON:0000464!1.09e-11!57;UBERON:0000473!9.71e-11!14;UBERON:0001008!2.65e-10!19;UBERON:0004872!4.35e-10!33;UBERON:0006554!6.99e-10!18;UBERON:0003101!1.26e-09!16;UBERON:0000079!1.26e-09!16;UBERON:0003135!1.28e-09!15;UBERON:0003103!2.76e-09!43;UBERON:0002113!1.89e-08!14;UBERON:0003918!1.89e-08!14;UBERON:0011143!1.89e-08!14;UBERON:0005095!1.89e-08!14;UBERON:0007687!1.89e-08!14;UBERON:0000474!2.47e-08!9;UBERON:0000466!5.49e-08!79;UBERON:0007100!1.24e-07!18;UBERON:0000948!1.24e-07!18;UBERON:0005498!1.24e-07!18;UBERON:0004140!1.24e-07!18;UBERON:0009881!1.24e-07!18;UBERON:0004141!1.24e-07!18;UBERON:0003084!1.24e-07!18;UBERON:0007005!1.24e-07!18;UBERON:0004139!1.24e-07!18;UBERON:0004291!1.24e-07!18;UBERON:0003134!1.88e-07!8;UBERON:0002075!1.97e-07!19;UBERON:0005177!3.08e-07!79
|tfbs_overrepresentation_for_novel_motifs=1.11639,0.161863,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.616096,1.25386,0.542749,0.575086,1.12363,0.599731,0.315771,0,0.795315,0.291368,4.00558,0.731589,0.374752,0.27937,0.598814,0.80655,0.419327,0.62766,0.184473,0.516511,1.63164,0.145661,0.50223,0.897561,2.19526,0.166577,2.33037,1.10671,0.279977,0.57142,0.258564,0.652422,0.800988,0.507468,0.0742755,0.317766,0.0275764,0.469348,1.70029,1.31862,0.0609361,0.917701,0.777641,0.654933,0.139618,1.04034,1.0579,1.47583,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.608073,0.0869413,1.09164,1.55661,4.48984,0.166511,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,0.580284,0.975495,0.0369809,0.042613,0.877485,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,0.589174,0.913319,0.71485,0.399703,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.990132,0.547992,1.27206,0.796976,1.12953,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,1.67446,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.886471,0.0736236,1.04192,0.243291,1.5029,1.12411,0.655955,0.874089,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,2.14328,0.573477,0.433127
|tfbs_overrepresentation_for_novel_motifs=1.11639,0.161863,0.411716,0.480627,0.299217,0.495263,0.587291,0.206208,0.616096,1.25386,0.542749,0.575086,1.12363,0.599731,0.315771,0,0.795315,0.291368,4.00558,0.731589,0.374752,0.27937,0.598814,0.80655,0.419327,0.62766,0.184473,0.516511,1.63164,0.145661,0.50223,0.897561,2.19526,0.166577,2.33037,1.10671,0.279977,0.57142,0.258564,0.652422,0.800988,0.507468,0.0742755,0.317766,0.0275764,0.469348,1.70029,1.31862,0.0609361,0.917701,0.777641,0.654933,0.139618,1.04034,1.0579,1.47583,0.356236,0.56214,0.176152,0.604914,0.877332,0.664501,0.226529,0.766235,0.618279,0.807219,1.19497,1.54543,0.872612,1.39786,0.392734,0.608073,0.0869413,1.09164,1.55661,4.48984,0.166511,0.703064,0.859987,0.378988,0.212973,0.812889,0.663039,0.580284,0.975495,0.0369809,0.042613,0.877485,0.719558,1.70793,1.26498,0.980512,0.910485,0.305079,0.254625,0.237542,0.589174,0.913319,0.71485,0.399703,0.280055,0.897279,1.02279,0.778243,0.777175,0.507021,0.837607,0.528416,0.383871,0.376549,0.430942,1.02459,0.990132,0.547992,1.27206,0.796976,1.12953,0.484437,0.796633,0.276329,1.09707,0.745011,0.629509,1.67446,1.32639,0.863723,0.595563,0.903645,1.19345,0.308038,1.00568,0.473246,1.16374,0.620831,1.29374,0.0806013,0.446555,0.508896,1.24438,2.07659,1.67603,1.19971,0.641722,0.908128,0.770616,0.507927,0.717753,2.03691,0.448938,0.300961,0.886471,0.0736236,1.04192,0.243291,1.5029,1.12411,0.655955,0.874089,0.435579,0.446272,1.25393,0.974632,0.864173,0.428662,0.767269,0.612377,2.14328,0.573477,0.433127
|tfbs_overrepresentation_jaspar=MA0003.1;0.54119,MA0004.1;2.09829,MA0006.1;0.311391,MA0007.1;0.465969,MA0009.1;0.92425,MA0014.1;2.85278,MA0017.1;0.337808,MA0019.1;0.740036,MA0024.1;0.880057,MA0025.1;1.15921,MA0027.1;2.57545,MA0028.1;0.321735,MA0029.1;0.858105,MA0030.1;0.864739,MA0031.1;0.828781,MA0038.1;0.62758,MA0040.1;0.936879,MA0041.1;0.404721,MA0042.1;0.391504,MA0043.1;1.02178,MA0046.1;0.960497,MA0048.1;0.801219,MA0050.1;0.520357,MA0051.1;0.636645,MA0052.1;0.945011,MA0055.1;0.362005,MA0056.1;0,MA0057.1;0.376102,MA0058.1;3.642,MA0059.1;4.79037,MA0060.1;0.232592,MA0061.1;0.724575,MA0063.1;0,MA0066.1;0.616444,MA0067.1;1.27078,MA0068.1;0.121435,MA0069.1;0.945354,MA0070.1;0.93557,MA0071.1;0.519509,MA0072.1;0.927016,MA0073.1;1.3018,MA0074.1;2.4233,MA0076.1;0.356883,MA0077.1;0.905143,MA0078.1;0.670113,MA0081.1;0.420276,MA0083.1;1.02098,MA0084.1;1.59945,MA0087.1;0.977537,MA0088.1;0.0841779,MA0089.1;0,MA0090.1;0.446539,MA0091.1;0.494398,MA0092.1;0.446857,MA0093.1;3.30666,MA0095.1;0,MA0098.1;0,MA0100.1;0.568369,MA0101.1;0.406019,MA0103.1;0.348572,MA0105.1;0.162418,MA0106.1;0.677988,MA0107.1;0.342432,MA0108.2;0.763162,MA0109.1;0,MA0111.1;4.09134,MA0113.1;0.649407,MA0114.1;0.259463,MA0115.1;1.0246,MA0116.1;0.311187,MA0117.1;0.992087,MA0119.1;0.40661,MA0122.1;1.01209,MA0124.1;1.21735,MA0125.1;1.14291,MA0130.1;0,MA0131.1;0.735438,MA0132.1;0,MA0133.1;0,MA0135.1;1.05845,MA0136.1;0.600242,MA0139.1;0.202522,MA0140.1;0.568252,MA0141.1;0.368264,MA0142.1;0.814115,MA0143.1;0.665982,MA0144.1;0.262477,MA0145.1;0.304732,MA0146.1;0.0256827,MA0147.1;2.12106,MA0148.1;0.49752,MA0149.1;0.411562,MA0062.2;0.167299,MA0035.2;1.40435,MA0039.2;2.09945,MA0138.2;1.72682,MA0002.2;0.205289,MA0137.2;0.365364,MA0104.2;1.82979,MA0047.2;0.626803,MA0112.2;0.0910939,MA0065.2;0.633155,MA0150.1;0.465855,MA0151.1;0,MA0152.1;0.626912,MA0153.1;2.43888,MA0154.1;0.126143,MA0155.1;0.102995,MA0156.1;0.356017,MA0157.1;0.781683,MA0158.1;0,MA0159.1;0.776527,MA0160.1;0.50056,MA0161.1;0,MA0162.1;0.302441,MA0163.1;0.519779,MA0164.1;0.600609,MA0080.2;0.343316,MA0018.2;1.48306,MA0099.2;0.721008,MA0079.2;0.432076,MA0102.2;1.65195,MA0258.1;0.246285,MA0259.1;2.06728,MA0442.1;0
}}
}}

Revision as of 12:56, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr2:104966436..104966455,+p7@Wt1
Mm9::chr2:104966465..104966479,+p6@Wt1
Mm9::chr2:104966510..104966538,-p2@ENSMUST00000174870
Mm9::chr2:104966545..104966586,-p1@ENSMUST00000174870
Mm9::chr2:104966662..104966673,+p4@Wt1
Mm9::chr2:104966766..104966786,+p1@Wt1
Mm9::chr2:105003277..105003280,+p5@Wt1


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:0001823mesonephros development0.0102996767654632
GO:0008584male gonad development0.0213350447284595
GO:0046546development of primary male sexual characteristics0.0213350447284595
GO:0007530sex determination0.0213350447284595
GO:0007281germ cell development0.0213350447284595
GO:0046661male sex differentiation0.0213350447284595
GO:0001570vasculogenesis0.0213350447284595
GO:0030855epithelial cell differentiation0.0231742727222922
GO:0001656metanephros development0.0248128576622523
GO:0008406gonad development0.0248128576622523
GO:0048608reproductive structure development0.0248128576622523
GO:0045137development of primary sexual characteristics0.0248908855165361
GO:0007548sex differentiation0.0254273270147373
GO:0001822kidney development0.0254273270147373
GO:0043010camera-type eye development0.0254273270147373
GO:0001655urogenital system development0.0254273270147373
GO:0003006reproductive developmental process0.0260521235832305
GO:0001654eye development0.0297546217668937
GO:0045786negative regulation of progression through cell cycle0.0314411185472035
GO:0002009morphogenesis of an epithelium0.0316715060537994
GO:0048514blood vessel morphogenesis0.039291359512693
GO:0000074regulation of progression through cell cycle0.039291359512693
GO:0007423sensory organ development0.039291359512693
GO:0045944positive regulation of transcription from RNA polymerase II promoter0.039291359512693
GO:0001568blood vessel development0.039291359512693
GO:0022414reproductive process0.039291359512693
GO:0001944vasculature development0.039291359512693
GO:0045893positive regulation of transcription, DNA-dependent0.0434057806544521
GO:0007276gamete generation0.0443951584718242
GO:0009888tissue development0.0455682669017463
GO:0045941positive regulation of transcription0.0455682669017463
GO:0045935positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0455682669017463
GO:0019953sexual reproduction0.0455682669017463



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
body cavity4.99e-2037
body cavity or lining4.99e-2037
body cavity precursor4.32e-1938
anatomical cavity3.31e-1839
reproductive structure2.03e-1726
reproductive system2.03e-1726
reproductive organ1.57e-1624
gonad3.48e-1418
gonad primordium3.48e-1418
external genitalia2.56e-1317
indifferent external genitalia2.56e-1317
indifferent gonad2.56e-1317
anatomical space1.09e-1157
testis9.71e-1114
renal system2.65e-1019
splanchnic layer of lateral plate mesoderm4.35e-1033
urinary system structure6.99e-1018
male organism1.26e-0916
male reproductive system1.26e-0916
male reproductive organ1.28e-0915
compound organ2.76e-0943
kidney1.89e-0814
kidney mesenchyme1.89e-0814
upper urinary tract1.89e-0814
kidney rudiment1.89e-0814
kidney field1.89e-0814
female reproductive system2.47e-089
immaterial anatomical entity5.49e-0879
primary circulatory organ1.24e-0718
heart1.24e-0718
primitive heart tube1.24e-0718
primary heart field1.24e-0718
anterior lateral plate mesoderm1.24e-0718
heart tube1.24e-0718
heart primordium1.24e-0718
cardiac mesoderm1.24e-0718
cardiogenic plate1.24e-0718
heart rudiment1.24e-0718
female reproductive organ1.88e-078
viscus1.97e-0719
trunk region element3.08e-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)
MA0003.10.54119
MA0004.12.09829
MA0006.10.311391
MA0007.10.465969
MA0009.10.92425
MA0014.12.85278
MA0017.10.337808
MA0019.10.740036
MA0024.10.880057
MA0025.11.15921
MA0027.12.57545
MA0028.10.321735
MA0029.10.858105
MA0030.10.864739
MA0031.10.828781
MA0038.10.62758
MA0040.10.936879
MA0041.10.404721
MA0042.10.391504
MA0043.11.02178
MA0046.10.960497
MA0048.10.801219
MA0050.10.520357
MA0051.10.636645
MA0052.10.945011
MA0055.10.362005
MA0056.10
MA0057.10.376102
MA0058.13.642
MA0059.14.79037
MA0060.10.232592
MA0061.10.724575
MA0063.10
MA0066.10.616444
MA0067.11.27078
MA0068.10.121435
MA0069.10.945354
MA0070.10.93557
MA0071.10.519509
MA0072.10.927016
MA0073.11.3018
MA0074.12.4233
MA0076.10.356883
MA0077.10.905143
MA0078.10.670113
MA0081.10.420276
MA0083.11.02098
MA0084.11.59945
MA0087.10.977537
MA0088.10.0841779
MA0089.10
MA0090.10.446539
MA0091.10.494398
MA0092.10.446857
MA0093.13.30666
MA0095.10
MA0098.10
MA0100.10.568369
MA0101.10.406019
MA0103.10.348572
MA0105.10.162418
MA0106.10.677988
MA0107.10.342432
MA0108.20.763162
MA0109.10
MA0111.14.09134
MA0113.10.649407
MA0114.10.259463
MA0115.11.0246
MA0116.10.311187
MA0117.10.992087
MA0119.10.40661
MA0122.11.01209
MA0124.11.21735
MA0125.11.14291
MA0130.10
MA0131.10.735438
MA0132.10
MA0133.10
MA0135.11.05845
MA0136.10.600242
MA0139.10.202522
MA0140.10.568252
MA0141.10.368264
MA0142.10.814115
MA0143.10.665982
MA0144.10.262477
MA0145.10.304732
MA0146.10.0256827
MA0147.12.12106
MA0148.10.49752
MA0149.10.411562
MA0062.20.167299
MA0035.21.40435
MA0039.22.09945
MA0138.21.72682
MA0002.20.205289
MA0137.20.365364
MA0104.21.82979
MA0047.20.626803
MA0112.20.0910939
MA0065.20.633155
MA0150.10.465855
MA0151.10
MA0152.10.626912
MA0153.12.43888
MA0154.10.126143
MA0155.10.102995
MA0156.10.356017
MA0157.10.781683
MA0158.10
MA0159.10.776527
MA0160.10.50056
MA0161.10
MA0162.10.302441
MA0163.10.519779
MA0164.10.600609
MA0080.20.343316
MA0018.21.48306
MA0099.20.721008
MA0079.20.432076
MA0102.21.65195
MA0258.10.246285
MA0259.12.06728
MA0442.10
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