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MCL coexpression mm9:686: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0004177!1.01e-22!29;UBERON:0005057!1.01e-22!29;UBERON:0002370!2.77e-18!23;UBERON:0000974!2.77e-18!23;UBERON:0004807!2.77e-18!23;UBERON:0005058!2.77e-18!23;UBERON:0003351!2.77e-18!23;UBERON:0009113!2.77e-18!23;UBERON:0003295!2.77e-18!23;UBERON:0009722!2.77e-18!23;UBERON:0005562!2.77e-18!23;UBERON:0007690!2.77e-18!23;UBERON:0000077!4.83e-18!35;UBERON:0006562!2.25e-17!24;UBERON:0003408!2.25e-17!24;UBERON:0001557!2.25e-17!24;UBERON:0001042!2.25e-17!24;UBERON:0008814!2.25e-17!24;UBERON:0009145!2.25e-17!24;UBERON:0000072!4.71e-15!27;UBERON:0002390!1.35e-14!45;UBERON:0003061!1.35e-14!45;UBERON:0002193!2.17e-13!48;UBERON:0002405!2.17e-13!48;UBERON:0000063!7.99e-11!35;UBERON:0007811!1.98e-10!36;UBERON:0003081!8.70e-10!87;UBERON:0003929!9.39e-09!55;UBERON:0000065!9.49e-09!41;UBERON:0002368!1.09e-08!60;UBERON:0001004!1.84e-08!42;UBERON:0000153!3.45e-08!43;UBERON:0001041!5.21e-08!80;UBERON:0002530!1.07e-07!65
|ontology_enrichment_uberon=UBERON:0004177!1.01e-22!29;UBERON:0005057!1.01e-22!29;UBERON:0002370!2.77e-18!23;UBERON:0000974!2.77e-18!23;UBERON:0004807!2.77e-18!23;UBERON:0005058!2.77e-18!23;UBERON:0003351!2.77e-18!23;UBERON:0009113!2.77e-18!23;UBERON:0003295!2.77e-18!23;UBERON:0009722!2.77e-18!23;UBERON:0005562!2.77e-18!23;UBERON:0007690!2.77e-18!23;UBERON:0000077!4.83e-18!35;UBERON:0006562!2.25e-17!24;UBERON:0003408!2.25e-17!24;UBERON:0001557!2.25e-17!24;UBERON:0001042!2.25e-17!24;UBERON:0008814!2.25e-17!24;UBERON:0009145!2.25e-17!24;UBERON:0000072!4.71e-15!27;UBERON:0002390!1.35e-14!45;UBERON:0003061!1.35e-14!45;UBERON:0002193!2.17e-13!48;UBERON:0002405!2.17e-13!48;UBERON:0000063!7.99e-11!35;UBERON:0007811!1.98e-10!36;UBERON:0003081!8.70e-10!87;UBERON:0003929!9.39e-09!55;UBERON:0000065!9.49e-09!41;UBERON:0002368!1.09e-08!60;UBERON:0001004!1.84e-08!42;UBERON:0000153!3.45e-08!43;UBERON:0001041!5.21e-08!80;UBERON:0002530!1.07e-07!65
|tfbs_overrepresentation_for_novel_motifs=0.321524,0.883225,0.807108,0.360062,0.580303,0.373426,1.16061,1.27916,0.816027,0.0244487,1.071,1.13606,0.393382,0.470194,1.15381,0,0.656089,0.564478,1.209,0.451901,1.34675,0.954669,0.469335,0.577226,0.822446,0.496413,1.16975,1.01819,0.238759,0.271461,0.379806,0.754912,0.191698,0.0942651,0.214608,0.386349,0.184038,0.443753,0.166348,0.143746,0.196807,0.38461,0.890234,0.215898,0.249283,0.349801,0.578773,1.05036,0.772185,0.677281,0.639101,0.522137,0.259389,0.894161,0.911367,0.47699,0.249055,0.435119,0.68053,1.19606,0.735292,0.531188,0.854737,0.628155,0.487593,0.667546,1.04613,1.3932,0.730718,1.24673,0.281085,0.404236,0.639498,0.944464,0.0968968,0.0893951,0.646602,0.567793,0.718494,0.74114,0.80832,0.673009,0.529804,0.764135,0.830765,0.0593483,0.0149522,0.96859,0.583509,1.55487,1.11522,0.835661,0.767462,0.205117,0.163126,1.43327,0.122617,0.770215,0.57902,0.86751,0.184103,0.754637,0.87698,0.639679,0.638654,0.3842,0.696857,0.403887,0.273261,0.266818,0.315128,0.878738,0.26996,1.08155,1.12221,0.195318,0.0839537,0.363536,0.657356,0.181004,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,0.466292,0.760818,1.04463,0.207624,2.00057,0.353344,1.01535,0.48999,1.14365,0.33206,0.329172,0.385921,1.09487,1.92247,1.5231,1.0508,1.27006,0.765172,0.632358,0.385031,0.581788,1.88287,0.331322,0.201635,0.0806411,0.0316649,0.895708,0.153911,0.489108,2.23791,0.523103,0.224422,0.319291,0.328917,1.1043,0.829923,0.722546,0.313083,0.629147,0.482049,0.53929,0.445669,0.350088
|tfbs_overrepresentation_for_novel_motifs=0.321524,0.883225,0.807108,0.360062,0.580303,0.373426,1.16061,1.27916,0.816027,0.0244487,1.071,1.13606,0.393382,0.470194,1.15381,0,0.656089,0.564478,1.209,0.451901,1.34675,0.954669,0.469335,0.577226,0.822446,0.496413,1.16975,1.01819,0.238759,0.271461,0.379806,0.754912,0.191698,0.0942651,0.214608,0.386349,0.184038,0.443753,0.166348,0.143746,0.196807,0.38461,0.890234,0.215898,0.249283,0.349801,0.578773,1.05036,0.772185,0.677281,0.639101,0.522137,0.259389,0.894161,0.911367,0.47699,0.249055,0.435119,0.68053,1.19606,0.735292,0.531188,0.854737,0.628155,0.487593,0.667546,1.04613,1.3932,0.730718,1.24673,0.281085,0.404236,0.639498,0.944464,0.0968968,0.0893951,0.646602,0.567793,0.718494,0.74114,0.80832,0.673009,0.529804,0.764135,0.830765,0.0593483,0.0149522,0.96859,0.583509,1.55487,1.11522,0.835661,0.767462,0.205117,0.163126,1.43327,0.122617,0.770215,0.57902,0.86751,0.184103,0.754637,0.87698,0.639679,0.638654,0.3842,0.696857,0.403887,0.273261,0.266818,0.315128,0.878738,0.26996,1.08155,1.12221,0.195318,0.0839537,0.363536,0.657356,0.181004,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,0.466292,0.760818,1.04463,0.207624,2.00057,0.353344,1.01535,0.48999,1.14365,0.33206,0.329172,0.385921,1.09487,1.92247,1.5231,1.0508,1.27006,0.765172,0.632358,0.385031,0.581788,1.88287,0.331322,0.201635,0.0806411,0.0316649,0.895708,0.153911,0.489108,2.23791,0.523103,0.224422,0.319291,0.328917,1.1043,0.829923,0.722546,0.313083,0.629147,0.482049,0.53929,0.445669,0.350088
|tfbs_overrepresentation_jaspar=MA0003.1;0.347165,MA0004.1;0.360508,MA0006.1;0.210471,MA0007.1;0.346734,MA0009.1;0.780842,MA0014.1;0.00520703,MA0017.1;0.658116,MA0019.1;0.603066,MA0024.1;0.737933,MA0025.1;1.01089,MA0027.1;2.42079,MA0028.1;0.219287,MA0029.1;0.716673,MA0030.1;1.71791,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;0.509074,MA0050.1;0.396459,MA0051.1;0.504875,MA0052.1;0.801048,MA0055.1;3.59269,MA0056.1;0,MA0057.1;0.059732,MA0058.1;0.273976,MA0059.1;0.28489,MA0060.1;0.446031,MA0061.1;0.504772,MA0063.1;0,MA0066.1;0.485868,MA0067.1;1.12095,MA0068.1;0.836551,MA0069.1;0.801381,MA0070.1;0.791856,MA0071.1;1.02422,MA0072.1;0.783532,MA0073.1;0.593688,MA0074.1;0.451832,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;0.14959,MA0089.1;0,MA0090.1;0.877277,MA0091.1;0.372635,MA0092.1;0.329444,MA0093.1;0.226349,MA0095.1;0,MA0098.1;0,MA0100.1;0.440912,MA0101.1;0.292867,MA0103.1;0.67982,MA0105.1;0.304995,MA0106.1;0.543967,MA0107.1;0.66744,MA0108.2;0.625209,MA0109.1;0,MA0111.1;0.342068,MA0113.1;0.516916,MA0114.1;0.500166,MA0115.1;0.878749,MA0116.1;0.210297,MA0117.1;1.97331,MA0119.1;3.07475,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;1.12231,MA0141.1;2.04423,MA0142.1;0.674191,MA0143.1;0.53259,MA0144.1;0.169559,MA0145.1;0.163161,MA0146.1;0.642452,MA0147.1;0.179496,MA0148.1;3.58649,MA0149.1;0.2978,MA0062.2;0.0948004,MA0035.2;1.1319,MA0039.2;0.647421,MA0138.2;0.590987,MA0002.2;1.27458,MA0137.2;0.713675,MA0104.2;0.134457,MA0047.2;2.14642,MA0112.2;0.663994,MA0065.2;0.163769,MA0150.1;0.346631,MA0151.1;0,MA0152.1;0.495709,MA0153.1;0.92832,MA0154.1;0.0653255,MA0155.1;2.67775,MA0156.1;0.248865,MA0157.1;0.642984,MA0158.1;0,MA0159.1;1.6576,MA0160.1;0.986076,MA0161.1;0,MA0162.1;0.134999,MA0163.1;0.439212,MA0164.1;0.471016,MA0080.2;0.237846,MA0018.2;0.480226,MA0099.2;1.42938,MA0079.2;0.0983396,MA0102.2;1.49914,MA0258.1;0.156336,MA0259.1;0.170828,MA0442.1;0
}}
}}

Revision as of 12:09, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:19438492..19438529,-p1@uc007enj.1
Mm9::chr11:88486943..88486975,-p@chr11:88486943..88486975
-
Mm9::chr15:81853206..81853231,+p7@Xrcc6
Mm9::chr15:81853256..81853270,+p9@Xrcc6
Mm9::chr15:81853287..81853302,+p10@Xrcc6
Mm9::chr15:81853353..81853364,+p13@Xrcc6
Mm9::chr15:86065302..86065315,+p@chr15:86065302..86065315
+
Mm9::chr5:114282539..114282554,-p@chr5:114282539..114282554
-
Mm9::chr9:103328951..103328961,+p@chr9:103328951..103328961
+
Mm9::chr9:103328967..103328977,+p@chr9:103328967..103328977
+


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:0005958DNA-dependent protein kinase complex0.00230099161781625
GO:0006303double-strand break repair via nonhomologous end joining0.00402673533117844
GO:0000726non-recombinational repair0.00402673533117844
GO:0005941unlocalized protein complex0.00402673533117844
GO:0004003ATP-dependent DNA helicase activity0.0046019832356325
GO:0003678DNA helicase activity0.00657426176518928
GO:0006302double-strand break repair0.00657426176518928
GO:0008094DNA-dependent ATPase activity0.009203966471265
GO:0006310DNA recombination0.01840793294253
GO:0008026ATP-dependent helicase activity0.01840793294253
GO:0004386helicase activity0.0263568130768043
GO:0006281DNA repair0.0358571193776366
GO:0042623ATPase activity, coupled0.0375349257656276
GO:0006974response to DNA damage stimulus0.0375349257656276
GO:0009719response to endogenous stimulus0.0375349257656276
GO:0016887ATPase activity0.0375349257656276



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
hemopoietic organ1.01e-2229
immune organ1.01e-2229
thymus2.77e-1823
neck2.77e-1823
respiratory system epithelium2.77e-1823
hemolymphoid system gland2.77e-1823
pharyngeal epithelium2.77e-1823
thymic region2.77e-1823
pharyngeal gland2.77e-1823
entire pharyngeal arch endoderm2.77e-1823
thymus primordium2.77e-1823
early pharyngeal endoderm2.77e-1823
mixed endoderm/mesoderm-derived structure4.83e-1835
pharynx2.25e-1724
gland of gut2.25e-1724
upper respiratory tract2.25e-1724
chordate pharynx2.25e-1724
pharyngeal arch system2.25e-1724
pharyngeal region of foregut2.25e-1724
segment of respiratory tract4.71e-1527
hematopoietic system1.35e-1445
blood island1.35e-1445
hemolymphoid system2.17e-1348
immune system2.17e-1348
organ segment7.99e-1135
craniocervical region1.98e-1036
lateral plate mesoderm8.70e-1087
gut epithelium9.39e-0955
respiratory tract9.49e-0941
endocrine gland1.09e-0860
respiratory system1.84e-0842
anterior region of body3.45e-0843
foregut5.21e-0880
gland1.07e-0765


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)
MA0003.10.347165
MA0004.10.360508
MA0006.10.210471
MA0007.10.346734
MA0009.10.780842
MA0014.10.00520703
MA0017.10.658116
MA0019.10.603066
MA0024.10.737933
MA0025.11.01089
MA0027.12.42079
MA0028.10.219287
MA0029.10.716673
MA0030.11.71791
MA0031.10.688336
MA0038.10.496338
MA0040.10.79313
MA0041.10.291712
MA0042.10.279998
MA0043.10.875991
MA0046.10.816137
MA0048.10.509074
MA0050.10.396459
MA0051.10.504875
MA0052.10.801048
MA0055.13.59269
MA0056.10
MA0057.10.059732
MA0058.10.273976
MA0059.10.28489
MA0060.10.446031
MA0061.10.504772
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.10.836551
MA0069.10.801381
MA0070.10.791856
MA0071.11.02422
MA0072.10.783532
MA0073.10.593688
MA0074.10.451832
MA0076.10.249619
MA0077.10.762273
MA0078.10.536502
MA0081.10.305576
MA0083.10.875209
MA0084.11.44691
MA0087.10.832758
MA0088.10.14959
MA0089.10
MA0090.10.877277
MA0091.10.372635
MA0092.10.329444
MA0093.10.226349
MA0095.10
MA0098.10
MA0100.10.440912
MA0101.10.292867
MA0103.10.67982
MA0105.10.304995
MA0106.10.543967
MA0107.10.66744
MA0108.20.625209
MA0109.10
MA0111.10.342068
MA0113.10.516916
MA0114.10.500166
MA0115.10.878749
MA0116.10.210297
MA0117.11.97331
MA0119.13.07475
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
MA0140.11.12231
MA0141.12.04423
MA0142.10.674191
MA0143.10.53259
MA0144.10.169559
MA0145.10.163161
MA0146.10.642452
MA0147.10.179496
MA0148.13.58649
MA0149.10.2978
MA0062.20.0948004
MA0035.21.1319
MA0039.20.647421
MA0138.20.590987
MA0002.21.27458
MA0137.20.713675
MA0104.20.134457
MA0047.22.14642
MA0112.20.663994
MA0065.20.163769
MA0150.10.346631
MA0151.10
MA0152.10.495709
MA0153.10.92832
MA0154.10.0653255
MA0155.12.67775
MA0156.10.248865
MA0157.10.642984
MA0158.10
MA0159.11.6576
MA0160.10.986076
MA0161.10
MA0162.10.134999
MA0163.10.439212
MA0164.10.471016
MA0080.20.237846
MA0018.20.480226
MA0099.21.42938
MA0079.20.0983396
MA0102.21.49914
MA0258.10.156336
MA0259.10.170828
MA0442.10
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