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MCL coexpression mm9:836: Difference between revisions

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{{MCL_coexpression_mm9
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|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000468!2.02e-11!333;UBERON:0005157!9.87e-09!20;UBERON:0002048!1.08e-08!14;UBERON:0000117!1.08e-08!14;UBERON:0000171!1.08e-08!14;UBERON:0000170!1.08e-08!14;UBERON:0005597!1.08e-08!14;UBERON:0000118!1.08e-08!14;UBERON:0002410!2.18e-07!9;UBERON:0005153!7.41e-07!17
|tfbs_overrepresentation_for_novel_motifs=1.66765,0.0206456,0.330161,0.394491,0.227651,0.40827,0.495658,0.146465,0.154135,0.133458,0.453212,1.21524,0.88117,0.507558,0.24249,0,1.66303,0.22065,0.419123,0.528436,0.296085,0.403891,0.50668,0.64218,0.337218,0.534339,0.801525,1.09532,1.35822,0.319094,0.414842,0.796599,0.218674,0.364174,0.242923,3.24453,0.210533,0.480503,0.559915,0.967553,0.224094,0.419787,0.163087,0.244285,0.158271,0.383899,0.618203,0.443479,0.573356,0.271021,0.679429,1.37808,1.05886,0.937018,0.954342,0.514504,0.279148,0.471658,0.770972,0.512521,0.776777,0.569793,0.163832,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,2.87596,0.31262,0.151245,0.0512949,0.987652,1.22652,0.349958,0.364033,0.607043,0.759798,0.299972,0.152219,0.713779,0.568383,1.38499,0.873141,0.204425,1.44422,1.09342,0.623015,1.60001,1.15927,0.878077,0.809272,0.232894,0.551605,0.515495,0.14449,0.812053,0.618454,0.0816605,0.210602,0.796322,0.919715,0.680015,0.678976,1.89067,0.737915,1.95923,1.48974,0.806647,0.348012,0.921485,0.301014,0.458194,1.16629,0.222515,0.265919,0.398075,0.697928,0.207304,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,2.17277,0.802564,2.4656,0.663857,0.90286,0.387557,1.05894,0.527782,1.18781,0.0467191,0.362565,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,1.613,1.07771,0.621266,1.92834,0.364791,0.229209,1.10522,0.369078,0.938577,0.178329,0.526881,1.01974,0.561556,0.253271,0.352329,0.950885,1.1483,0.872292,0.763895,0.345891,0.669337,0.519673,0.209556,0.482466,0.0435162
|tfbs_overrepresentation_jaspar=MA0003.1;0.00972621,MA0004.1;0.394951,MA0006.1;0.670874,MA0007.1;0.38073,MA0009.1;0.82278,MA0014.1;0.67203,MA0017.1;0.26239,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;0.534262,MA0040.1;0.835181,MA0041.1;0.323687,MA0042.1;0.311486,MA0043.1;0.918718,MA0046.1;0.858391,MA0048.1;0.993388,MA0050.1;3.92312,MA0051.1;0.542972,MA0052.1;0.84317,MA0055.1;0.0198867,MA0056.1;0,MA0057.1;0.258928,MA0058.1;0.305206,MA0059.1;0.316585,MA0060.1;0.169058,MA0061.1;1.07655,MA0063.1;0,MA0066.1;0.523573,MA0067.1;1.16502,MA0068.1;1.9687,MA0069.1;0.843506,MA0070.1;0.833895,MA0071.1;0.431174,MA0072.1;0.825495,MA0073.1;0.0217447,MA0074.1;0.488775,MA0076.1;0.279739,MA0077.1;0.804033,MA0078.1;0.575205,MA0081.1;0.338098,MA0083.1;0.917931,MA0084.1;1.49188,MA0087.1;0.87515,MA0088.1;2.66548,MA0089.1;0,MA0090.1;0.362551,MA0091.1;1.04993,MA0092.1;0.95209,MA0093.1;0.2553,MA0095.1;0,MA0098.1;0,MA0100.1;0.477594,MA0101.1;1.56277,MA0103.1;0.272167,MA0105.1;0.720048,MA0106.1;1.42499,MA0107.1;2.08048,MA0108.2;0.665343,MA0109.1;0,MA0111.1;0.375908,MA0113.1;0.555251,MA0114.1;0.19245,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;0.29014,MA0142.1;0.714976,MA0143.1;0.571221,MA0144.1;0.195095,MA0145.1;4.81123,MA0146.1;0.0111657,MA0147.1;0.205697,MA0148.1;0.410398,MA0149.1;0.330018,MA0062.2;0.113962,MA0035.2;0.482026,MA0039.2;0.043355,MA0138.2;0.630612,MA0002.2;0.145685,MA0137.2;0.287486,MA0104.2;0.157347,MA0047.2;0.533516,MA0112.2;1.17898,MA0065.2;0.0545595,MA0150.1;0.380623,MA0151.1;0,MA0152.1;0.53362,MA0153.1;0.971406,MA0154.1;0.581988,MA0155.1;0.0631765,MA0156.1;0.278949,MA0157.1;0.683365,MA0158.1;0,MA0159.1;0.214506,MA0160.1;0.413266,MA0161.1;0,MA0162.1;0.0672805,MA0163.1;0.0124565,MA0164.1;0.508398,MA0080.2;0.267388,MA0018.2;0.51781,MA0099.2;0.624421,MA0079.2;0.0191848,MA0102.2;1.5442,MA0258.1;0.180934,MA0259.1;0.571417,MA0442.1;0
}}

Latest revision as of 15:58, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr18:38760990..38761009,-p1@Spry4
Mm9::chr3:57379682..57379758,-p1@Wwtr1
Mm9::chr9:117161183..117161200,-p6@Rbms3
Mm9::chr9:117161229..117161243,-p8@Rbms3
Mm9::chr9:117161244..117161301,-p3@Rbms3
Mm9::chr9:117161310..117161334,-p5@Rbms3
Mm9::chr9:117161463..117161501,-p4@Rbms3
Mm9::chr9:117161568..117161607,-p1@Rbms3
Mm9::chr9:117161783..117161842,-p2@Rbms3


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:0045599negative regulation of fat cell differentiation0.0354990684841625



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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
autonomic neuron2.18e-079

Uber Anatomy
Ontology termp-valuen
multi-cellular organism2.02e-11333
epithelial fold9.87e-0920
lung1.08e-0814
respiratory tube1.08e-0814
respiration organ1.08e-0814
pair of lungs1.08e-0814
lung primordium1.08e-0814
lung bud1.08e-0814
autonomic nervous system2.18e-079
epithelial bud7.41e-0717


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)
MA0003.10.00972621
MA0004.10.394951
MA0006.10.670874
MA0007.10.38073
MA0009.10.82278
MA0014.10.67203
MA0017.10.26239
MA0019.10.642876
MA0024.10.779446
MA0025.11.05446
MA0027.12.46647
MA0028.10.24786
MA0029.10.757957
MA0030.10.764448
MA0031.10.729293
MA0038.10.534262
MA0040.10.835181
MA0041.10.323687
MA0042.10.311486
MA0043.10.918718
MA0046.10.858391
MA0048.10.993388
MA0050.13.92312
MA0051.10.542972
MA0052.10.84317
MA0055.10.0198867
MA0056.10
MA0057.10.258928
MA0058.10.305206
MA0059.10.316585
MA0060.10.169058
MA0061.11.07655
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.11.9687
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.10.0217447
MA0074.10.488775
MA0076.10.279739
MA0077.10.804033
MA0078.10.575205
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.12.66548
MA0089.10
MA0090.10.362551
MA0091.11.04993
MA0092.10.95209
MA0093.10.2553
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.11.56277
MA0103.10.272167
MA0105.10.720048
MA0106.11.42499
MA0107.12.08048
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
MA0114.10.19245
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
MA0141.10.29014
MA0142.10.714976
MA0143.10.571221
MA0144.10.195095
MA0145.14.81123
MA0146.10.0111657
MA0147.10.205697
MA0148.10.410398
MA0149.10.330018
MA0062.20.113962
MA0035.20.482026
MA0039.20.043355
MA0138.20.630612
MA0002.20.145685
MA0137.20.287486
MA0104.20.157347
MA0047.20.533516
MA0112.21.17898
MA0065.20.0545595
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.581988
MA0155.10.0631765
MA0156.10.278949
MA0157.10.683365
MA0158.10
MA0159.10.214506
MA0160.10.413266
MA0161.10
MA0162.10.0672805
MA0163.10.0124565
MA0164.10.508398
MA0080.20.267388
MA0018.20.51781
MA0099.20.624421
MA0079.20.0191848
MA0102.21.5442
MA0258.10.180934
MA0259.10.571417
MA0442.10
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