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MCL coexpression mm9:743: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0003133!4.48e-15!24;UBERON:0005156!5.38e-15!26;UBERON:0000990!5.38e-15!26;UBERON:0002323!4.33e-14!37;UBERON:0004458!4.33e-14!37;UBERON:0003886!1.98e-13!38;UBERON:0000991!3.75e-13!18;UBERON:0005564!3.75e-13!18;UBERON:0002553!8.30e-13!39;UBERON:0004176!3.64e-12!17;UBERON:0009196!3.64e-12!17;UBERON:0009117!3.64e-12!17;UBERON:0000473!1.89e-09!14;UBERON:0000464!2.13e-09!57;UBERON:0003135!1.65e-08!15;UBERON:0004872!5.71e-08!33;UBERON:0007100!6.06e-08!18;UBERON:0000948!6.06e-08!18;UBERON:0005498!6.06e-08!18;UBERON:0004140!6.06e-08!18;UBERON:0009881!6.06e-08!18;UBERON:0004141!6.06e-08!18;UBERON:0003084!6.06e-08!18;UBERON:0007005!6.06e-08!18;UBERON:0004139!6.06e-08!18;UBERON:0004291!6.06e-08!18;UBERON:0000474!6.21e-08!9;UBERON:0003101!1.08e-07!16;UBERON:0000079!1.08e-07!16;UBERON:0003103!2.20e-07!43;UBERON:0003134!4.71e-07!8
|ontology_enrichment_uberon=UBERON:0003133!4.48e-15!24;UBERON:0005156!5.38e-15!26;UBERON:0000990!5.38e-15!26;UBERON:0002323!4.33e-14!37;UBERON:0004458!4.33e-14!37;UBERON:0003886!1.98e-13!38;UBERON:0000991!3.75e-13!18;UBERON:0005564!3.75e-13!18;UBERON:0002553!8.30e-13!39;UBERON:0004176!3.64e-12!17;UBERON:0009196!3.64e-12!17;UBERON:0009117!3.64e-12!17;UBERON:0000473!1.89e-09!14;UBERON:0000464!2.13e-09!57;UBERON:0003135!1.65e-08!15;UBERON:0004872!5.71e-08!33;UBERON:0007100!6.06e-08!18;UBERON:0000948!6.06e-08!18;UBERON:0005498!6.06e-08!18;UBERON:0004140!6.06e-08!18;UBERON:0009881!6.06e-08!18;UBERON:0004141!6.06e-08!18;UBERON:0003084!6.06e-08!18;UBERON:0007005!6.06e-08!18;UBERON:0004139!6.06e-08!18;UBERON:0004291!6.06e-08!18;UBERON:0000474!6.21e-08!9;UBERON:0003101!1.08e-07!16;UBERON:0000079!1.08e-07!16;UBERON:0003103!2.20e-07!43;UBERON:0003134!4.71e-07!8
|tfbs_overrepresentation_for_novel_motifs=1.55081,0.352573,0.297937,0.360062,0.200163,0.373426,0.458558,0.124431,0.816027,4.27651,0.417132,0.447169,2.5119,1.18563,0.214197,0,0.656089,0.19356,0.736624,0.786777,0.26524,0.0365724,1.18379,0.198877,0.304728,0.496413,0.107695,0.392919,1.24776,0.0790295,0.379806,0.754912,1.06562,0.0942651,1.80612,7.64393,0.184038,0.443753,0.166348,2.01695,0.196807,0.38461,0.0320468,0.215898,0.249283,0.349801,0.578773,0.407653,0.0244624,0.241306,0.639101,0.522137,0.0747297,0.894161,0.911367,1.20022,0.249055,0.435119,0.101408,0.47505,0.735292,1.31585,0.140453,0.628155,0.487593,0.667546,1.04613,1.3932,0.730718,1.24673,2.15451,0.128829,0.03967,0.944464,2.20686,13.4877,1.07748,1.39333,0.718494,0.268962,0.129727,0.673009,0.529804,0.119727,0.830765,0.0122854,0.893815,3.97313,0.583509,1.55487,1.11522,0.835661,0.767462,0.205117,0.490417,0.149272,0.777003,0.770215,0.57902,7.64073,0.184103,0.754637,0.87698,0.639679,0.638654,0.3842,0.696857,0.403887,0.273261,0.266818,0.315128,0.878738,2.09779,1.08155,1.12221,0.5687,4.55445,9.24473,0.657356,0.181004,0.949798,0.607824,0.498153,2.38052,1.17594,0.722111,0.466292,0.760818,1.04463,0.207624,0.86025,0.353344,1.01535,1.22806,1.14365,0.0358067,0.329172,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,0.385031,0.581788,1.88287,0.331322,0.201635,0.0806411,0.129005,0.895708,0.153911,0.489108,0.976367,0.523103,0.637798,0.319291,0.328917,1.1043,0.829923,0.722546,0.313083,0.629147,0.482049,3.08151,0.445669,2.25318
|tfbs_overrepresentation_for_novel_motifs=1.55081,0.352573,0.297937,0.360062,0.200163,0.373426,0.458558,0.124431,0.816027,4.27651,0.417132,0.447169,2.5119,1.18563,0.214197,0,0.656089,0.19356,0.736624,0.786777,0.26524,0.0365724,1.18379,0.198877,0.304728,0.496413,0.107695,0.392919,1.24776,0.0790295,0.379806,0.754912,1.06562,0.0942651,1.80612,7.64393,0.184038,0.443753,0.166348,2.01695,0.196807,0.38461,0.0320468,0.215898,0.249283,0.349801,0.578773,0.407653,0.0244624,0.241306,0.639101,0.522137,0.0747297,0.894161,0.911367,1.20022,0.249055,0.435119,0.101408,0.47505,0.735292,1.31585,0.140453,0.628155,0.487593,0.667546,1.04613,1.3932,0.730718,1.24673,2.15451,0.128829,0.03967,0.944464,2.20686,13.4877,1.07748,1.39333,0.718494,0.268962,0.129727,0.673009,0.529804,0.119727,0.830765,0.0122854,0.893815,3.97313,0.583509,1.55487,1.11522,0.835661,0.767462,0.205117,0.490417,0.149272,0.777003,0.770215,0.57902,7.64073,0.184103,0.754637,0.87698,0.639679,0.638654,0.3842,0.696857,0.403887,0.273261,0.266818,0.315128,0.878738,2.09779,1.08155,1.12221,0.5687,4.55445,9.24473,0.657356,0.181004,0.949798,0.607824,0.498153,2.38052,1.17594,0.722111,0.466292,0.760818,1.04463,0.207624,0.86025,0.353344,1.01535,1.22806,1.14365,0.0358067,0.329172,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,0.385031,0.581788,1.88287,0.331322,0.201635,0.0806411,0.129005,0.895708,0.153911,0.489108,0.976367,0.523103,0.637798,0.319291,0.328917,1.1043,0.829923,0.722546,0.313083,0.629147,0.482049,3.08151,0.445669,2.25318
|tfbs_overrepresentation_jaspar=MA0003.1;2.62288,MA0004.1;3.49532,MA0006.1;0.210471,MA0007.1;0.346734,MA0009.1;0.780842,MA0014.1;1.092,MA0017.1;0.233089,MA0019.1;0.603066,MA0024.1;4.22942,MA0025.1;1.01089,MA0027.1;2.42079,MA0028.1;0.219287,MA0029.1;0.716673,MA0030.1;0.723093,MA0031.1;0.688336,MA0038.1;0.496338,MA0040.1;0.79313,MA0041.1;0.291712,MA0042.1;0.279998,MA0043.1;0.875991,MA0046.1;0.816137,MA0048.1;1.31676,MA0050.1;0.396459,MA0051.1;2.17709,MA0052.1;0.801048,MA0055.1;0.866263,MA0056.1;0,MA0057.1;0.817159,MA0058.1;2.11833,MA0059.1;1.41888,MA0060.1;0.145297,MA0061.1;2.21331,MA0063.1;0,MA0066.1;0.485868,MA0067.1;1.12095,MA0068.1;0.0621035,MA0069.1;0.801381,MA0070.1;0.791856,MA0071.1;0.395679,MA0072.1;0.783532,MA0073.1;10.697,MA0074.1;5.18261,MA0076.1;0.249619,MA0077.1;0.762273,MA0078.1;0.536502,MA0081.1;0.305576,MA0083.1;0.875209,MA0084.1;1.44691,MA0087.1;0.832758,MA0088.1;1.39028,MA0089.1;0,MA0090.1;0.329158,MA0091.1;0.372635,MA0092.1;0.329444,MA0093.1;4.35966,MA0095.1;0,MA0098.1;0,MA0100.1;0.440912,MA0101.1;0.795627,MA0103.1;0.242398,MA0105.1;0.632131,MA0106.1;0.543967,MA0107.1;1.24141,MA0108.2;0.625209,MA0109.1;0,MA0111.1;1.62353,MA0113.1;0.516916,MA0114.1;0.167085,MA0115.1;0.878749,MA0116.1;0.210297,MA0117.1;0.846964,MA0119.1;0.293392,MA0122.1;0.866511,MA0124.1;1.06819,MA0125.1;0.994853,MA0130.1;0,MA0131.1;0.598671,MA0132.1;0,MA0133.1;0,MA0135.1;0.911905,MA0136.1;0.470672,MA0139.1;0.121562,MA0140.1;0.440804,MA0141.1;0.259554,MA0142.1;0.674191,MA0143.1;0.53259,MA0144.1;0.169559,MA0145.1;0.163161,MA0146.1;0.0389394,MA0147.1;3.04834,MA0148.1;0.375491,MA0149.1;3.10307,MA0062.2;0.0948004,MA0035.2;0.44524,MA0039.2;1.09654,MA0138.2;0.590987,MA0002.2;0.123715,MA0137.2;0.257017,MA0104.2;1.9417,MA0047.2;0.495607,MA0112.2;0.0422488,MA0065.2;0.373167,MA0150.1;0.346631,MA0151.1;0,MA0152.1;0.495709,MA0153.1;0.92832,MA0154.1;0.232525,MA0155.1;0.0498353,MA0156.1;0.248865,MA0157.1;0.642984,MA0158.1;0,MA0159.1;1.05,MA0160.1;0.378276,MA0161.1;0,MA0162.1;3.76186,MA0163.1;0.439212,MA0164.1;0.471016,MA0080.2;1.9307,MA0018.2;0.480226,MA0099.2;0.584892,MA0079.2;4.99335,MA0102.2;1.49914,MA0258.1;0.156336,MA0259.1;0.981631,MA0442.1;0
}}
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Revision as of 12:14, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr2:104966636..104966641,+p12@Wt1
Mm9::chr2:104966659..104966672,-p1@AI314831
Mm9::chr2:104966683..104966700,-p3@AI314831
Mm9::chr2:104966713..104966727,-p2@AI314831
Mm9::chr2:104966874..104966907,+p2@Wt1
Mm9::chr2:104966909..104966920,+p8@Wt1
Mm9::chr2:104966933..104966966,+p3@Wt1
Mm9::chr2:104966983..104966990,+p11@Wt1
Mm9::chr7:103661125..103661139,+p@chr7:103661125..103661139
+
Mm9::chr8:40383519..40383531,+p2@Gm6213


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
reproductive organ4.48e-1524
reproductive structure5.38e-1526
reproductive system5.38e-1526
body cavity4.33e-1437
body cavity or lining4.33e-1437
body cavity precursor1.98e-1338
gonad3.75e-1318
gonad primordium3.75e-1318
anatomical cavity8.30e-1339
external genitalia3.64e-1217
indifferent external genitalia3.64e-1217
indifferent gonad3.64e-1217
testis1.89e-0914
anatomical space2.13e-0957
male reproductive organ1.65e-0815
splanchnic layer of lateral plate mesoderm5.71e-0833
primary circulatory organ6.06e-0818
heart6.06e-0818
primitive heart tube6.06e-0818
primary heart field6.06e-0818
anterior lateral plate mesoderm6.06e-0818
heart tube6.06e-0818
heart primordium6.06e-0818
cardiac mesoderm6.06e-0818
cardiogenic plate6.06e-0818
heart rudiment6.06e-0818
female reproductive system6.21e-089
male organism1.08e-0716
male reproductive system1.08e-0716
compound organ2.20e-0743
female reproductive organ4.71e-078


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)
MA0003.12.62288
MA0004.13.49532
MA0006.10.210471
MA0007.10.346734
MA0009.10.780842
MA0014.11.092
MA0017.10.233089
MA0019.10.603066
MA0024.14.22942
MA0025.11.01089
MA0027.12.42079
MA0028.10.219287
MA0029.10.716673
MA0030.10.723093
MA0031.10.688336
MA0038.10.496338
MA0040.10.79313
MA0041.10.291712
MA0042.10.279998
MA0043.10.875991
MA0046.10.816137
MA0048.11.31676
MA0050.10.396459
MA0051.12.17709
MA0052.10.801048
MA0055.10.866263
MA0056.10
MA0057.10.817159
MA0058.12.11833
MA0059.11.41888
MA0060.10.145297
MA0061.12.21331
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.10.0621035
MA0069.10.801381
MA0070.10.791856
MA0071.10.395679
MA0072.10.783532
MA0073.110.697
MA0074.15.18261
MA0076.10.249619
MA0077.10.762273
MA0078.10.536502
MA0081.10.305576
MA0083.10.875209
MA0084.11.44691
MA0087.10.832758
MA0088.11.39028
MA0089.10
MA0090.10.329158
MA0091.10.372635
MA0092.10.329444
MA0093.14.35966
MA0095.10
MA0098.10
MA0100.10.440912
MA0101.10.795627
MA0103.10.242398
MA0105.10.632131
MA0106.10.543967
MA0107.11.24141
MA0108.20.625209
MA0109.10
MA0111.11.62353
MA0113.10.516916
MA0114.10.167085
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
MA0136.10.470672
MA0139.10.121562
MA0140.10.440804
MA0141.10.259554
MA0142.10.674191
MA0143.10.53259
MA0144.10.169559
MA0145.10.163161
MA0146.10.0389394
MA0147.13.04834
MA0148.10.375491
MA0149.13.10307
MA0062.20.0948004
MA0035.20.44524
MA0039.21.09654
MA0138.20.590987
MA0002.20.123715
MA0137.20.257017
MA0104.21.9417
MA0047.20.495607
MA0112.20.0422488
MA0065.20.373167
MA0150.10.346631
MA0151.10
MA0152.10.495709
MA0153.10.92832
MA0154.10.232525
MA0155.10.0498353
MA0156.10.248865
MA0157.10.642984
MA0158.10
MA0159.11.05
MA0160.10.378276
MA0161.10
MA0162.13.76186
MA0163.10.439212
MA0164.10.471016
MA0080.21.9307
MA0018.20.480226
MA0099.20.584892
MA0079.24.99335
MA0102.21.49914
MA0258.10.156336
MA0259.10.981631
MA0442.10
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