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MCL coexpression mm9:834: Difference between revisions

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{{MCL_coexpression_mm9
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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.127160916153114,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0482820047261801,0,0.240944651400519,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.145528461145601,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0711694759496908,0.0655375003561515,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.458996264357154,0.682413811162695,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.429926417524237,0.341658512969439,0.261808060351695,0.294963273112386,0.249188311215674,0.304002696497688,0.287545982608219,0.50697486371057,0.659461493415343,0.53349767349843,0.43587302681043,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.769649854451254,0.732070248718084,0.837333440907334,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
|gostat_on_MCL_coexpression=GO:0008270;zinc ion binding;0.0321341290354308;269424,99377,23808,233902!GO:0043283;biopolymer metabolic process;0.0321341290354308;252870,269424,99377,23808,233902!GO:0046914;transition metal ion binding;0.0430705596479491;269424,99377,23808,233902!
|ontology_enrichment_celltype=CL:0000349!4.70e-14!3;CL:0000351!4.70e-14!3
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000991!1.52e-41!18;UBERON:0005564!1.52e-41!18;UBERON:0003133!1.04e-40!24;UBERON:0004176!4.48e-38!17;UBERON:0009196!4.48e-38!17;UBERON:0009117!4.48e-38!17;UBERON:0005156!2.24e-37!26;UBERON:0000990!2.24e-37!26;UBERON:0000473!9.05e-34!14;UBERON:0003135!2.11e-31!15;UBERON:0003101!2.48e-29!16;UBERON:0000079!2.48e-29!16;UBERON:0002323!5.27e-19!37;UBERON:0004458!5.27e-19!37;UBERON:0003886!1.93e-18!38;UBERON:0002553!6.61e-18!39;UBERON:0000358!4.70e-14!3;UBERON:0000307!4.70e-14!3;UBERON:0007010!4.70e-14!3;UBERON:0005631!4.25e-13!3;UBERON:0000478!4.25e-13!3;UBERON:0000158!4.25e-13!3;UBERON:0000464!1.75e-11!57;UBERON:0001987!1.38e-09!2;UBERON:0003124!1.38e-09!2;UBERON:0004340!1.38e-09!2;UBERON:0003134!3.03e-08!8;UBERON:0000926!6.94e-08!120;UBERON:0004120!6.94e-08!120;UBERON:0006603!6.94e-08!120;UBERON:0000466!1.34e-07!79;UBERON:0000474!2.43e-07!9
|tfbs_overrepresentation_for_novel_motifs=0.354643,0.227469,0.330161,0.394491,0.645379,0.40827,0.495658,0.146465,0.468136,0.314043,0.453212,1.21524,0.146657,0.507558,0.24249,0,0.696644,0.22065,0.134657,0.0703872,0.802917,0.403891,0.50668,0.226287,0.337218,0.534339,0.801525,0.428336,0.268347,0.319094,0.414842,0.796599,0.218674,0.364174,1.26347,1.40616,0.604998,0.480503,0.191662,0.500908,0.224094,0.419787,0.371854,1.2686,0.536558,0.383899,0.618203,0.443479,0.0330279,0.271021,0.679429,0.560572,0.30602,0.937018,0.954342,0.514504,0.279148,0.471658,0.384731,0.512521,0.776777,0.569793,0.163832,0.668331,0.525334,0.708248,1.08987,1.43807,0.772155,1.29123,0.840217,0.151245,0.0512949,0.987652,0.371787,0.107966,0.113315,0.607043,0.759798,1.47357,0.463363,0.713779,0.568383,0.436063,0.873141,0.0176817,0.092683,1.61229,0.623015,1.60001,1.15927,0.878077,0.809272,0.232894,0.551605,0.515495,0.871972,0.812053,0.618454,0.278788,0.210602,0.796322,0.919715,0.680015,0.678976,0.419366,0.737915,0.439611,0.30446,0.297733,0.348012,0.921485,0.301014,0.458194,1.16629,0.633313,0.10952,0.398075,0.697928,1.12703,0.993019,0.647706,0.536114,0.606154,1.22022,0.763454,3.20775,0.802564,1.08836,0.235546,0.90286,0.387557,2.40589,0.527782,1.18781,0.177062,1.6953,0.421136,1.13883,1.96797,1.5682,1.09456,0.547855,0.806961,0.672593,0.420221,0.621266,1.92834,0.364791,0.229209,0.098204,0.161645,0.938577,0.178329,0.526881,1.01974,0.561556,0.705025,0.352329,0.362302,1.1483,0.872292,0.763895,0.345891,0.669337,0.519673,0.209556,1.21195,1.31706
}}

Latest revision as of 15:58, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr16:8792424..8792441,-p5@Usp7
Mm9::chr16:8792459..8792470,-p11@Usp7
Mm9::chr2:168592591..168592604,-p2@Sall4
Mm9::chr3:41359618..41359629,+p14@Phf17
Mm9::chr7:134891622..134891634,+p6@Fbxl19
Mm9::chr7:134891651..134891669,+p2@Fbxl19
Mm9::chr8:26958093..26958148,-p2@Ash2l
Mm9::chr8:34627132..34627150,+p4@Tex15
Mm9::chr9:114421557..114421561,-p@chr9:114421557..114421561
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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:0008270zinc ion binding0.0321341290354308
GO:0043283biopolymer metabolic process0.0321341290354308
GO:0046914transition metal ion binding0.0430705596479491



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
extraembryonic cell4.70e-143
trophoblast cell4.70e-143

Uber Anatomy
Ontology termp-valuen
gonad1.52e-4118
gonad primordium1.52e-4118
reproductive organ1.04e-4024
external genitalia4.48e-3817
indifferent external genitalia4.48e-3817
indifferent gonad4.48e-3817
reproductive structure2.24e-3726
reproductive system2.24e-3726
testis9.05e-3414
male reproductive organ2.11e-3115
male organism2.48e-2916
male reproductive system2.48e-2916
body cavity5.27e-1937
body cavity or lining5.27e-1937
body cavity precursor1.93e-1838
anatomical cavity6.61e-1839
blastocyst4.70e-143
blastula4.70e-143
cleaving embryo4.70e-143
extraembryonic membrane4.25e-133
extraembryonic structure4.25e-133
membranous layer4.25e-133
anatomical space1.75e-1157
placenta1.38e-092
chorion1.38e-092
allantois1.38e-092
female reproductive organ3.03e-088
mesoderm6.94e-08120
mesoderm-derived structure6.94e-08120
presumptive mesoderm6.94e-08120
immaterial anatomical entity1.34e-0779
female reproductive system2.43e-079


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)
MA0003.10.0343274
MA0004.11.02263
MA0006.10.238555
MA0007.10.38073
MA0009.10.82278
MA0014.10.0421798
MA0017.10.726051
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
MA0046.11.99676
MA0048.10.0824771
MA0050.10.431976
MA0051.10.542972
MA0052.10.84317
MA0055.10.0198867
MA0056.10
MA0057.10.0745664
MA0058.10.305206
MA0059.10.316585
MA0060.11.55044
MA0061.10.194456
MA0063.10
MA0066.10.523573
MA0067.11.16502
MA0068.10.266547
MA0069.10.843506
MA0070.10.833895
MA0071.10.431174
MA0072.10.825495
MA0073.10.0771206
MA0074.10.488775
MA0076.10.279739
MA0077.10.804033
MA0078.10.575205
MA0081.10.338098
MA0083.10.917931
MA0084.11.49188
MA0087.10.87515
MA0088.11.5772
MA0089.10
MA0090.10.951436
MA0091.10.407455
MA0092.10.362847
MA0093.11.30984
MA0095.10
MA0098.10
MA0100.10.477594
MA0101.10.324888
MA0103.10.272167
MA0105.10.109964
MA0106.10.582805
MA0107.10.266586
MA0108.20.665343
MA0109.10
MA0111.10.375908
MA0113.10.555251
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
MA0131.11.54167
MA0132.10
MA0133.10
MA0135.10.954884
MA0136.11.26662
MA0139.10.143341
MA0140.10.477483
MA0141.10.29014
MA0142.11.70108
MA0143.11.40057
MA0144.14.03621
MA0145.10.200183
MA0146.10.148686
MA0147.10.593505
MA0148.10.410398
MA0149.10.330018
MA0062.21.21132
MA0035.20.482026
MA0039.20.618828
MA0138.20.630612
MA0002.20.447007
MA0137.20.783415
MA0104.20.926067
MA0047.20.533516
MA0112.20.200175
MA0065.20.200864
MA0150.10.380623
MA0151.10
MA0152.10.53362
MA0153.10.971406
MA0154.10.276788
MA0155.10.490492
MA0156.12.14366
MA0157.10.683365
MA0158.10
MA0159.10.614411
MA0160.11.06259
MA0161.10
MA0162.10.0672805
MA0163.10.0600297
MA0164.10.508398
MA0080.22.08461
MA0018.20.51781
MA0099.20.624421
MA0079.20.0340753
MA0102.21.5442
MA0258.10.533988
MA0259.10.571417
MA0442.10
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