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MCL coexpression mm9:725: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0006412;translation;0.00218338187021981;78655,218693,67204!GO:0003743;translation initiation factor activity;0.0023664660051835;78655,67204!GO:0009059;macromolecule biosynthetic process;0.00245155188948107;78655,218693,67204!GO:0008135;translation factor activity, nucleic acid binding;0.00262078524398316;78655,67204!GO:0044249;cellular biosynthetic process;0.0033130541374977;78655,218693,67204!GO:0009058;biosynthetic process;0.00676030477367006;78655,218693,67204!GO:0006413;translational initiation;0.0466916131618276;67204!GO:0044267;cellular protein metabolic process;0.0466916131618276;78655,218693,67204!GO:0044260;cellular macromolecule metabolic process;0.0466916131618276;78655,218693,67204!GO:0010467;gene expression;0.0466916131618276;78655,218693,67204!GO:0019538;protein metabolic process;0.0466916131618276;78655,218693,67204!}}
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initiation factor activity;0.0023664660051835;78655,67204!GO:0009059;macromolecule biosynthetic process;0.00245155188948107;78655,218693,67204!GO:0008135;translation factor activity, nucleic acid binding;0.00262078524398316;78655,67204!GO:0044249;cellular biosynthetic process;0.0033130541374977;78655,218693,67204!GO:0009058;biosynthetic process;0.00676030477367006;78655,218693,67204!GO:0006413;translational initiation;0.0466916131618276;67204!GO:0044267;cellular protein metabolic process;0.0466916131618276;78655,218693,67204!GO:0044260;cellular macromolecule metabolic process;0.0466916131618276;78655,218693,67204!GO:0010467;gene expression;0.0466916131618276;78655,218693,67204!GO:0019538;protein metabolic process;0.0466916131618276;78655,218693,67204!|ontology_enrichment_celltype=|ontology_enrichment_disease=|ontology_enrichment_uberon=UBERON:0000991!2.06e-12!18;UBERON:0005564!2.06e-12!18;UBERON:0003133!6.75e-12!24;UBERON:0004176!1.81e-11!17;UBERON:0009196!1.81e-11!17;UBERON:0009117!1.81e-11!17;UBERON:0005156!1.82e-10!26;UBERON:0000990!1.82e-10!26;UBERON:0000473!3.85e-10!14;UBERON:0003135!3.52e-09!15;UBERON:0003101!2.40e-08!16;UBERON:0000079!2.40e-08!16|tfbs_overrepresentation_for_novel_motifs=0.321524,0.588611,0.297937,0.360062,0.580303,0.373426,0.458558,0.124431,0.131493,0.10445,1.071,0.447169,0.124608,0.470194,0.214197,0,0.656089,0.564478,0.113609,0.0560853,0.26524,0.336916,1.18379,0.198877,0.304728,2.14909,0.107695,1.01819,0.238759,0.271461,0.379806,0.754912,0.191698,0.646834,0.214608,0.102262,0.541514,1.12869,0.963289,0.143746,0.196807,0.38461,1.28169,0.617704,0.119503,0.923221,0.578773,1.05036,0.255625,0.677281,0.639101,0.522137,0.550735,0.894161,0.911367,0.47699,0.249055,0.435119,0.332535,0.47505,0.735292,0.531188,0.433822,0.628155,1.22293,0.667546,1.04613,1.3932,0.730718,1.24673,0.281085,0.128829,1.41981,0.944464,0.659328,0.300089,0.313198,0.567793,0.718494,0.74114,0.129727,0.673009,0.529804,0.380754,0.830765,1.14518,3.66701,0.0791202,0.583509,1.55487,1.11522,0.835661,0.767462,0.205117,0.490417,0.892226,0.777003,0.770215,0.57902,0.234357,0.541671,0.754637,0.87698,0.639679,0.638654,1.77029,0.696857,0.403887,0.273261,0.266818,0.845852,0.878738,0.26996,0.421988,1.12221,0.195318,0.212667,0.363536,0.657356,0.534159,0.949798,0.607824,0.498153,0.566919,1.17594,0.722111,0.466292,0.760818,1.04463,0.207624,0.86025,0.353344,1.01535,0.48999,1.14365,0.33206,0.877308,0.385921,1.09487,1.92247,1.5231,1.0508,0.509663,0.765172,0.632358,0.385031,0.581788,1.88287,0.331322,2.45403,0.0806411,0.559158,0.895708,0.911723,0.489108,0.976367,0.523103,0.224422,0.855195,0.328917,1.1043,0.829923,0.722546,0.313083,0.629147,0.482049,0.53929,0.445669,0.809881|tfbs_overrepresentation_jaspar=MA0003.1;1.53513,MA0004.1;0.946922,MA0006.1;0.604851,MA0007.1;0.346734,MA0009.1;0.780842,MA0014.1;0.189966,MA0017.1;0.658116,MA0019.1;0.603066,MA0024.1;1.74864,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;0.509074,MA0050.1;0.396459,MA0051.1;0.504875,MA0052.1;0.801048,MA0055.1;0.17385,MA0056.1;0,MA0057.1;0.817159,MA0058.1;0.752621,MA0059.1;0.28489,MA0060.1;0.145297,MA0061.1;0.16896,MA0063.1;0,MA0066.1;0.485868,MA0067.1;1.12095,MA0068.1;0.22316,MA0069.1;0.801381,MA0070.1;0.791856,MA0071.1;0.395679,MA0072.1;0.783532,MA0073.1;1.53988,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;1.86507,MA0089.1;0,MA0090.1;0.329158,MA0091.1;0.372635,MA0092.1;0.329444,MA0093.1;0.642324,MA0095.1;0,MA0098.1;0,MA0100.1;0.440912,MA0101.1;0.292867,MA0103.1;0.242398,MA0105.1;1.0562,MA0106.1;1.34295,MA0107.1;0.237082,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;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;0.385513,MA0140.1;0.440804,MA0141.1;0.259554,MA0142.1;0.674191,MA0143.1;0.53259,MA0144.1;0.169559,MA0145.1;0.664015,MA0146.1;0.923066,MA0147.1;1.01679,MA0148.1;0.375491,MA0149.1;0.2978,MA0062.2;0.0948004,MA0035.2;0.44524,MA0039.2;2.69973,MA0138.2;0.590987,MA0002.2;0.123715,MA0137.2;0.257017,MA0104.2;0.418613,MA0047.2;0.495607,MA0112.2;0.163154,MA0065.2;0.665832,MA0150.1;0.346631,MA0151.1;0,MA0152.1;1.24029,MA0153.1;0.92832,MA0154.1;0.0653255,MA0155.1;0.416651,MA0156.1;0.248865,MA0157.1;0.642984,MA0158.1;0,MA0159.1;0.187774,MA0160.1;0.378276,MA0161.1;0,MA0162.1;1.39091,MA0163.1;0.679942,MA0164.1;0.471016,MA0080.2;1.2443,MA0018.2;0.480226,MA0099.2;0.584892,MA0079.2;4.01017,MA0102.2;1.49914,MA0258.1;0.473611,MA0259.1;0.50935,MA0442.1;0}}

Latest revision as of 15:47, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr13:120217297..120217311,+p7@Paip1
Mm9::chr16:8783471..8783495,-p@chr16:8783471..8783495
-
Mm9::chr17:23940582..23940651,+p@chr17:23940582..23940651
+
Mm9::chr2:10514804..10514818,+p@chr2:10514804..10514818
+
Mm9::chr2:121854280..121854299,+p2@Eif3j
Mm9::chr2:154718567..154718619,-p1@Eif2s2
p1@Gm9892
Mm9::chr2:154718623..154718630,-p2@Eif2s2
Mm9::chr4:132595425..132595440,+p8@Ahdc1
Mm9::chr8:28334286..28334305,-p@chr8:28334286..28334305
-
Mm9::chr8:44391224..44391234,-p@chr8:44391224..44391234
-


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:0006412translation0.00218338187021981
GO:0003743translation initiation factor activity0.0023664660051835
GO:0009059macromolecule biosynthetic process0.00245155188948107
GO:0008135translation factor activity, nucleic acid binding0.00262078524398316
GO:0044249cellular biosynthetic process0.0033130541374977
GO:0009058biosynthetic process0.00676030477367006
GO:0006413translational initiation0.0466916131618276
GO:0044267cellular protein metabolic process0.0466916131618276
GO:0044260cellular macromolecule metabolic process0.0466916131618276
GO:0010467gene expression0.0466916131618276
GO:0019538protein metabolic process0.0466916131618276



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
gonad2.06e-1218
gonad primordium2.06e-1218
reproductive organ6.75e-1224
external genitalia1.81e-1117
indifferent external genitalia1.81e-1117
indifferent gonad1.81e-1117
reproductive structure1.82e-1026
reproductive system1.82e-1026
testis3.85e-1014
male reproductive organ3.52e-0915
male organism2.40e-0816
male reproductive system2.40e-0816


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)
MA0003.11.53513
MA0004.10.946922
MA0006.10.604851
MA0007.10.346734
MA0009.10.780842
MA0014.10.189966
MA0017.10.658116
MA0019.10.603066
MA0024.11.74864
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
MA0048.10.509074
MA0050.10.396459
MA0051.10.504875
MA0052.10.801048
MA0055.10.17385
MA0056.10
MA0057.10.817159
MA0058.10.752621
MA0059.10.28489
MA0060.10.145297
MA0061.10.16896
MA0063.10
MA0066.10.485868
MA0067.11.12095
MA0068.10.22316
MA0069.10.801381
MA0070.10.791856
MA0071.10.395679
MA0072.10.783532
MA0073.11.53988
MA0074.10.451832
MA0076.10.249619
MA0077.10.762273
MA0078.10.536502
MA0081.10.305576
MA0083.10.875209
MA0084.11.44691
MA0087.10.832758
MA0088.11.86507
MA0089.10
MA0090.10.329158
MA0091.10.372635
MA0092.10.329444
MA0093.10.642324
MA0095.10
MA0098.10
MA0100.10.440912
MA0101.10.292867
MA0103.10.242398
MA0105.11.0562
MA0106.11.34295
MA0107.10.237082
MA0108.20.625209
MA0109.10
MA0111.10.342068
MA0113.10.516916
MA0114.10.500166
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
MA0139.10.385513
MA0140.10.440804
MA0141.10.259554
MA0142.10.674191
MA0143.10.53259
MA0144.10.169559
MA0145.10.664015
MA0146.10.923066
MA0147.11.01679
MA0148.10.375491
MA0149.10.2978
MA0062.20.0948004
MA0035.20.44524
MA0039.22.69973
MA0138.20.590987
MA0002.20.123715
MA0137.20.257017
MA0104.20.418613
MA0047.20.495607
MA0112.20.163154
MA0065.20.665832
MA0150.10.346631
MA0151.10
MA0152.11.24029
MA0153.10.92832
MA0154.10.0653255
MA0155.10.416651
MA0156.10.248865
MA0157.10.642984
MA0158.10
MA0159.10.187774
MA0160.10.378276
MA0161.10
MA0162.11.39091
MA0163.10.679942
MA0164.10.471016
MA0080.21.2443
MA0018.20.480226
MA0099.20.584892
MA0079.24.01017
MA0102.21.49914
MA0258.10.473611
MA0259.10.50935
MA0442.10
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