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MCL coexpression mm9:832: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002048!5.25e-11!14;UBERON:0000117!5.25e-11!14;UBERON:0000171!5.25e-11!14;UBERON:0000170!5.25e-11!14;UBERON:0005597!5.25e-11!14;UBERON:0000118!5.25e-11!14;UBERON:0005153!2.38e-08!17;UBERON:0005178!2.38e-08!17;UBERON:0005181!2.38e-08!17;UBERON:0002224!2.38e-08!17;UBERON:0000915!2.38e-08!17;UBERON:0008947!2.38e-08!17;UBERON:0003258!2.38e-08!17
|ontology_enrichment_uberon=UBERON:0002048!5.25e-11!14;UBERON:0000117!5.25e-11!14;UBERON:0000171!5.25e-11!14;UBERON:0000170!5.25e-11!14;UBERON:0005597!5.25e-11!14;UBERON:0000118!5.25e-11!14;UBERON:0005153!2.38e-08!17;UBERON:0005178!2.38e-08!17;UBERON:0005181!2.38e-08!17;UBERON:0002224!2.38e-08!17;UBERON:0000915!2.38e-08!17;UBERON:0008947!2.38e-08!17;UBERON:0003258!2.38e-08!17
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.433653,0.330161,0.394491,0.645379,0.40827,0.495658,0.146465,0.154135,0.133458,2.00501,1.21524,0.449446,0.507558,0.24249,0,0.696644,0.22065,0.134657,0.902262,0.296085,0.179861,0.50668,0.64218,0.337218,1.32254,0.402559,0.428336,0.268347,0.656973,0.414842,0.796599,0.624261,0.735537,1.26347,0.281474,0.210533,0.480503,1.06548,0.167387,1.85739,0.419787,0.371854,0.244285,0.812975,0.998423,0.618203,1.12809,1.30029,0.745859,0.679429,0.560572,0.633942,0.937018,0.954342,0.514504,0.764433,0.471658,1.25881,0.512521,0.776777,0.569793,0.492158,1.60412,0.525334,0.708248,1.08987,1.43807,1.81937,1.29123,0.840217,0.460931,1.14319,0.987652,0.116281,0.349958,1.20707,1.47595,0.759798,0.299972,0.152219,0.713779,0.568383,0.436063,0.873141,0.0176817,0.092683,0.0965007,0.623015,1.60001,1.15927,0.878077,0.809272,0.232894,1.66008,0.17334,0.444003,0.812053,0.618454,0.987389,1.78429,0.796322,0.919715,0.680015,0.678976,1.07585,0.737915,0.439611,0.821842,0.297733,0.919252,0.921485,0.301014,0.458194,1.16629,0.222515,0.265919,0.398075,0.697928,0.597328,0.993019,0.647706,2.27991,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,1.23559,0.90286,0.387557,1.05894,0.527782,1.18781,0.0467191,1.6953,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,0.364791,0.229209,0.32395,0.041769,0.938577,0.178329,0.526881,1.01974,0.561556,0.705025,0.352329,0.362302,1.1483,0.872292,0.763895,0.345891,0.669337,0.519673,0.209556,0.482466,0.0435162
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.433653,0.330161,0.394491,0.645379,0.40827,0.495658,0.146465,0.154135,0.133458,2.00501,1.21524,0.449446,0.507558,0.24249,0,0.696644,0.22065,0.134657,0.902262,0.296085,0.179861,0.50668,0.64218,0.337218,1.32254,0.402559,0.428336,0.268347,0.656973,0.414842,0.796599,0.624261,0.735537,1.26347,0.281474,0.210533,0.480503,1.06548,0.167387,1.85739,0.419787,0.371854,0.244285,0.812975,0.998423,0.618203,1.12809,1.30029,0.745859,0.679429,0.560572,0.633942,0.937018,0.954342,0.514504,0.764433,0.471658,1.25881,0.512521,0.776777,0.569793,0.492158,1.60412,0.525334,0.708248,1.08987,1.43807,1.81937,1.29123,0.840217,0.460931,1.14319,0.987652,0.116281,0.349958,1.20707,1.47595,0.759798,0.299972,0.152219,0.713779,0.568383,0.436063,0.873141,0.0176817,0.092683,0.0965007,0.623015,1.60001,1.15927,0.878077,0.809272,0.232894,1.66008,0.17334,0.444003,0.812053,0.618454,0.987389,1.78429,0.796322,0.919715,0.680015,0.678976,1.07585,0.737915,0.439611,0.821842,0.297733,0.919252,0.921485,0.301014,0.458194,1.16629,0.222515,0.265919,0.398075,0.697928,0.597328,0.993019,0.647706,2.27991,0.606154,1.22022,0.763454,0.503569,0.802564,1.08836,1.23559,0.90286,0.387557,1.05894,0.527782,1.18781,0.0467191,1.6953,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,0.364791,0.229209,0.32395,0.041769,0.938577,0.178329,0.526881,1.01974,0.561556,0.705025,0.352329,0.362302,1.1483,0.872292,0.763895,0.345891,0.669337,0.519673,0.209556,0.482466,0.0435162
|tfbs_overrepresentation_jaspar=MA0003.1;0.00143485,MA0004.1;0.394951,MA0006.1;0.238555,MA0007.1;0.38073,MA0009.1;0.82278,MA0014.1;0.119217,MA0017.1;1.3362,MA0019.1;0.642876,MA0024.1;0.779446,MA0025.1;1.05446,MA0027.1;2.46647,MA0028.1;0.24786,MA0029.1;0.757957,MA0030.1;0.764448,MA0031.1;0.729293,MA0038.1;1.32237,MA0040.1;0.835181,MA0041.1;0.323687,MA0042.1;0.311486,MA0043.1;0.918718,MA0046.1;0.858391,MA0048.1;0.281053,MA0050.1;0.431976,MA0051.1;1.34084,MA0052.1;0.84317,MA0055.1;0.424109,MA0056.1;0,MA0057.1;0.258928,MA0058.1;0.305206,MA0059.1;0.316585,MA0060.1;1.55044,MA0061.1;0.194456,MA0063.1;0,MA0066.1;1.29967,MA0067.1;1.16502,MA0068.1;0.077274,MA0069.1;0.843506,MA0070.1;0.833895,MA0071.1;0.431174,MA0072.1;0.825495,MA0073.1;0.0771206,MA0074.1;0.488775,MA0076.1;0.279739,MA0077.1;0.804033,MA0078.1;1.40897,MA0081.1;0.338098,MA0083.1;0.917931,MA0084.1;1.49188,MA0087.1;2.03111,MA0088.1;0.0492918,MA0089.1;0,MA0090.1;0.362551,MA0091.1;0.407455,MA0092.1;0.362847,MA0093.1;0.709711,MA0095.1;0,MA0098.1;0,MA0100.1;1.20151,MA0101.1;0.324888,MA0103.1;0.748482,MA0105.1;0.109964,MA0106.1;0.582805,MA0107.1;0.266586,MA0108.2;0.665343,MA0109.1;0,MA0111.1;0.980871,MA0113.1;1.36684,MA0114.1;0.561811,MA0115.1;0.921497,MA0116.1;0.238371,MA0117.1;0.88947,MA0119.1;0.325434,MA0122.1;0.909168,MA0124.1;1.11203,MA0125.1;1.03833,MA0130.1;0,MA0131.1;0.638414,MA0132.1;0,MA0133.1;0,MA0135.1;0.954884,MA0136.1;0.508047,MA0139.1;0.441109,MA0140.1;0.477483,MA0141.1;0.789442,MA0142.1;0.714976,MA0143.1;0.571221,MA0144.1;0.195095,MA0145.1;0.200183,MA0146.1;0.148686,MA0147.1;0.205697,MA0148.1;0.410398,MA0149.1;0.330018,MA0062.2;0.113962,MA0035.2;0.482026,MA0039.2;0.436553,MA0138.2;0.630612,MA0002.2;0.145685,MA0137.2;0.783415,MA0104.2;0.157347,MA0047.2;0.533516,MA0112.2;0.0543294,MA0065.2;0.200864,MA0150.1;0.380623,MA0151.1;0,MA0152.1;0.53362,MA0153.1;0.971406,MA0154.1;0.581988,MA0155.1;0.490492,MA0156.1;0.278949,MA0157.1;0.683365,MA0158.1;0,MA0159.1;0.214506,MA0160.1;0.413266,MA0161.1;0,MA0162.1;0.0143037,MA0163.1;0.0124565,MA0164.1;0.508398,MA0080.2;0.737531,MA0018.2;1.28741,MA0099.2;0.624421,MA0079.2;6.4867e-05,MA0102.2;1.5442,MA0258.1;0.533988,MA0259.1;0.196451,MA0442.1;0
}}
}}

Revision as of 12:23, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr16:44394918..44394939,+p2@Wdr52
Mm9::chr3:87552455..87552477,-p3@4933430H15Rik
Mm9::chr3:89866703..89866758,+p1@1700094D03Rik
Mm9::chr4:96453435..96453456,-p@chr4:96453435..96453456
-
Mm9::chr6:73171602..73171616,-p2@Dnahc6
Mm9::chr6:73171619..73171658,-p1@Dnahc6
Mm9::chr8:107951487..107951519,+p1@Lrrc36
Mm9::chr8:107951522..107951533,+p5@Lrrc36
Mm9::chr9:96425722..96425743,+p@chr9:96425722..96425743
+


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:0005858axonemal dynein complex0.0293698834960756
GO:0044447axoneme part0.0293698834960756
GO:0005930axoneme0.0293698834960756
GO:0030286dynein complex0.0293698834960756



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
lung5.25e-1114
respiratory tube5.25e-1114
respiration organ5.25e-1114
pair of lungs5.25e-1114
lung primordium5.25e-1114
lung bud5.25e-1114
epithelial bud2.38e-0817
thoracic cavity element2.38e-0817
thoracic segment organ2.38e-0817
thoracic cavity2.38e-0817
thoracic segment of trunk2.38e-0817
respiratory primordium2.38e-0817
endoderm of foregut2.38e-0817


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)
MA0003.10.00143485
MA0004.10.394951
MA0006.10.238555
MA0007.10.38073
MA0009.10.82278
MA0014.10.119217
MA0017.11.3362
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.10.24786
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.11.32237
MA0040.10.835181
MA0041.10.323687
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.10.281053
MA0050.10.431976
MA0051.11.34084
MA0052.10.84317
MA0055.10.424109
MA0056.10
MA0057.10.258928
MA0058.10.305206
MA0059.10.316585
MA0060.11.55044
MA0061.10.194456
MA0063.10
MA0066.11.29967
MA0067.11.16502
MA0068.10.077274
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.10.0771206
MA0074.10.488775
MA0076.10.279739
MA0077.10.804033
MA0078.11.40897
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.12.03111
MA0088.10.0492918
MA0089.10
MA0090.10.362551
MA0091.10.407455
MA0092.10.362847
MA0093.10.709711
MA0095.10
MA0098.10
MA0100.11.20151
MA0101.10.324888
MA0103.10.748482
MA0105.10.109964
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.980871
MA0113.11.36684
MA0114.10.561811
MA0115.10.921497
MA0116.10.238371
MA0117.10.88947
MA0119.10.325434
MA0122.10.909168
MA0124.11.11203
MA0125.11.03833
MA0130.10
MA0131.10.638414
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.10.508047
MA0139.10.441109
MA0140.10.477483
MA0141.10.789442
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.10.200183
MA0146.10.148686
MA0147.10.205697
MA0148.10.410398
MA0149.10.330018
MA0062.20.113962
MA0035.20.482026
MA0039.20.436553
MA0138.20.630612
MA0002.20.145685
MA0137.20.783415
MA0104.20.157347
MA0047.20.533516
MA0112.20.0543294
MA0065.20.200864
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.581988
MA0155.10.490492
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.10.0143037
MA0163.10.0124565
MA0164.10.508398
MA0080.20.737531
MA0018.21.28741
MA0099.20.624421
MA0079.26.4867e-05
MA0102.21.5442
MA0258.10.533988
MA0259.10.196451
MA0442.10
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