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MCL coexpression mm9:301: Difference between revisions

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{{MCL_coexpression_mm9
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biogenesis and assembly;5.11680186249144e-07;52513,66254,69663,59014,53414!GO:0022613;ribonucleoprotein complex biogenesis and assembly;3.20675718272105e-06;52513,66254,69663,59014,53414!GO:0005730;nucleolus;4.9783549932582e-06;52513,18432,64424,74111!GO:0016072;rRNA metabolic process;9.72423441477556e-06;52513,66254,69663!GO:0006364;rRNA processing;9.72423441477556e-06;52513,66254,69663!GO:0005634;nucleus;1.35386557805915e-05;101612,110816,66254,107094,53414,74111,52513,22185,68626,226169,18432,69663,59014,64424!GO:0003723;RNA binding;2.30020001477502e-05;52513,22185,226169,66254,69663,74111!GO:0006396;RNA processing;2.86814449429933e-05;52513,22185,68626,66254,69663!GO:0016070;RNA metabolic process;0.00418132620189929;66254,52513,22185,68626,226169,18432,69663,64424!GO:0043231;intracellular membrane-bound organelle;0.00418132620189929;101612,110816,66254,107094,53414,74111,52513,22185,68626,226169,18432,69663,59014,64424!GO:0043227;membrane-bound organelle;0.00418132620189929;101612,110816,66254,107094,53414,74111,52513,22185,68626,226169,18432,69663,59014,64424!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0057915285466571;66254,51797,52513,22185,68626,226169,18432,69663,64424!GO:0044428;nuclear part;0.0057915285466571;52513,22185,18432,64424,74111!GO:0031981;nuclear lumen;0.00651548456133426;52513,18432,64424,74111!GO:0006996;organelle organization and biogenesis;0.00855697563088129;52513,66254,69663,59014,53414!GO:0031974;membrane-enclosed lumen;0.00855697563088129;52513,18432,64424,74111!GO:0043233;organelle lumen;0.00855697563088129;52513,18432,64424,74111!GO:0010467;gene expression;0.00855697563088129;66254,52513,22185,68626,226169,18432,69663,64424!GO:0031074;nucleocytoplasmic shuttling complex;0.00855697563088129;18432!GO:0042564;NLS-dependent protein nuclear import complex;0.00855697563088129;18432!GO:0001651;dense fibrillar component;0.00855697563088129;!GO:0003676;nucleic acid binding;0.00929918789864357;66254,74111,52513,22185,226169,18432,69663,64424!GO:0043229;intracellular organelle;0.0121978450728034;101612,110816,66254,107094,53414,74111,52513,22185,68626,226169,18432,69663,59014,64424!GO:0043226;organelle;0.0121978450728034;101612,110816,66254,107094,53414,74111,52513,22185,68626,226169,18432,69663,59014,64424!GO:0003883;CTP synthase activity;0.0138156121431303;51797!GO:0030515;snoRNA binding;0.0138156121431303;!GO:0000179;rRNA (adenine-N6,N6-)-dimethyltransferase activity;0.0179509488968946;66254!GO:0016433;rRNA (adenine) methyltransferase activity;0.0179509488968946;66254!GO:0008649;rRNA methyltransferase activity;0.0179509488968946;66254!GO:0008026;ATP-dependent helicase activity;0.0181160658139124;52513,69663!GO:0000154;rRNA modification;0.0224270101912869;66254!GO:0009303;rRNA transcription;0.0271701114396692;64424!GO:0016779;nucleotidyltransferase activity;0.0285973935560174;18432,64424!GO:0004386;helicase 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|gostat_on_MCL_coexpression=GO:0042254;ribosome biogenesis and assembly;5.11680186249144e-07;52513,66254,69663,59014,53414!GO:0022613;ribonucleoprotein complex biogenesis and assembly;3.20675718272105e-06;52513,66254,69663,59014,53414!GO:0005730;nucleolus;4.9783549932582e-06;52513,18432,64424,74111!GO:0016072;rRNA metabolic process;9.72423441477556e-06;52513,66254,69663!GO:0006364;rRNA processing;9.72423441477556e-06;52513,66254,69663!GO:0005634;nucleus;1.35386557805915e-05;101612,110816,66254,107094,53414,74111,52513,22185,68626,226169,18432,69663,59014,64424!GO:0003723;RNA binding;2.30020001477502e-05;52513,22185,226169,66254,69663,74111!GO:0006396;RNA processing;2.86814449429933e-05;52513,22185,68626,66254,69663!GO:0016070;RNA metabolic process;0.00418132620189929;66254,52513,22185,68626,226169,18432,69663,64424!GO:0043231;intracellular membrane-bound organelle;0.00418132620189929;101612,110816,66254,107094,53414,74111,52513,22185,68626,226169,18432,69663,59014,64424!GO:0043227;membrane-bound organelle;0.00418132620189929;101612,110816,66254,107094,53414,74111,52513,22185,68626,226169,18432,69663,59014,64424!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0057915285466571;66254,51797,52513,22185,68626,226169,18432,69663,64424!GO:0044428;nuclear part;0.0057915285466571;52513,22185,18432,64424,74111!GO:0031981;nuclear lumen;0.00651548456133426;52513,18432,64424,74111!GO:0006996;organelle organization and biogenesis;0.00855697563088129;52513,66254,69663,59014,53414!GO:0031974;membrane-enclosed lumen;0.00855697563088129;52513,18432,64424,74111!GO:0043233;organelle lumen;0.00855697563088129;52513,18432,64424,74111!GO:0010467;gene expression;0.00855697563088129;66254,52513,22185,68626,226169,18432,69663,64424!GO:0031074;nucleocytoplasmic shuttling complex;0.00855697563088129;18432!GO:0042564;NLS-dependent protein nuclear import complex;0.00855697563088129;18432!GO:0001651;dense fibrillar component;0.00855697563088129;!GO:0003676;nucleic acid binding;0.00929918789864357;66254,74111,52513,22185,226169,18432,69663,64424!GO:0043229;intracellular organelle;0.0121978450728034;101612,110816,66254,107094,53414,74111,52513,22185,68626,226169,18432,69663,59014,64424!GO:0043226;organelle;0.0121978450728034;101612,110816,66254,107094,53414,74111,52513,22185,68626,226169,18432,69663,59014,64424!GO:0003883;CTP synthase activity;0.0138156121431303;51797!GO:0030515;snoRNA binding;0.0138156121431303;!GO:0000179;rRNA (adenine-N6,N6-)-dimethyltransferase activity;0.0179509488968946;66254!GO:0016433;rRNA (adenine) methyltransferase activity;0.0179509488968946;66254!GO:0008649;rRNA methyltransferase activity;0.0179509488968946;66254!GO:0008026;ATP-dependent helicase activity;0.0181160658139124;52513,69663!GO:0000154;rRNA modification;0.0224270101912869;66254!GO:0009303;rRNA transcription;0.0271701114396692;64424!GO:0016779;nucleotidyltransferase activity;0.0285973935560174;18432,64424!GO:0004386;helicase activity;0.0388005106397328;52513,69663!GO:0016043;cellular component organization and biogenesis;0.0408817001251616;52513,66254,18432,69663,59014,53414!
|ontology_enrichment_celltype=CL:0000988!2.89e-10!32;CL:0002032!2.89e-10!32;CL:0000037!2.89e-10!32;CL:0000566!2.89e-10!32;CL:0000837!2.89e-10!32;CL:0002242!2.08e-09!16;CL:0000542!1.97e-07!13;CL:0000051!1.97e-07!13;CL:0002031!2.94e-07!25;CL:0000838!7.24e-07!12;CL:0000034!9.02e-07!97
|ontology_enrichment_disease=
|ontology_enrichment_uberon=
|tfbs_overrepresentation_for_novel_motifs=1.48293,0.661951,0.531928,0.10379,0.125245,0.359101,0.955578,1.06294,0.525465,0.772291,1.36304,0.156977,0.491749,1.56893,0.141341,0,0.309751,0.28293,0.251913,0.296846,0.0558898,0.042472,2.97592,0.294801,0.549054,0.556347,0.233256,1.2696,0.687261,0.274542,1.21916,0.390688,0.517018,0.345661,2.89275,0.00164234,2.02999,0.469672,0.698183,0.177786,0.121493,0.117985,0.539272,0.0360344,0.545429,1.10422,0.697098,0.81779,0.100232,1.07572,0.803415,1.77168,0.628973,1.27306,0.526356,0.52404,0.183928,0.891812,0.21374,1.00074,0.97729,0.61508,0.339634,1.42919,2.32642,0.854326,0.648538,0.976882,0.370478,0.836509,0.489831,0.301094,0.660587,0.555978,1.47449,1.74329,0.191853,1.25857,0.360359,0.459928,0.150594,0.864154,0.213792,1.02261,1.15397,0.750187,0.0937328,0.0205384,0.253413,1.13385,0.712592,2.02686,0.401262,0.032222,0.0861131,0.0728776,0.280832,1.04151,0.697528,0.111549,0.262089,1.0128,0.495886,0.29676,0.802619,1.80149,2.45922,0.129587,0.815002,1.68721,0.273137,0.497436,0.211055,0.434758,0.719117,0.843445,0.452141,1.15674,0.31076,0.255342,0.560777,0.271955,0.559259,0.240971,0.769516,0.363346,0.506409,1.02418,1.55994,0.574009,0.481183,1.64467,0.620289,0.185736,0.739171,0.167784,0.293295,0.759822,0.693638,1.49553,1.10287,0.652839,0.199449,0.399329,0.791415,0.376878,1.29796,1.45635,0.0880519,0.552494,0.681533,0.728342,0.512441,0.385153,0.544151,0.584782,0.208987,0.0391866,0.0817634,1.02467,0.702412,0.454746,0.953986,0.570246,0.288496,0.180287,0.106601,0.472773,0.0784137
}}

Latest revision as of 15:03, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:77647847..77647900,-p1@Pwp2
Mm9::chr11:6167721..6167758,-p1@Ddx56
Mm9::chr11:64792527..64792612,+p1@Elac2
Mm9::chr11:72254843..72254888,+p1@Mybbp1a
Mm9::chr13:107737184..107737244,+p1@Dimt1
Mm9::chr13:3610310..3610364,-p1@BC016423
Mm9::chr13:54691408..54691450,-p1@Nop16
Mm9::chr17:24844562..24844606,-p1@Tbl3
Mm9::chr17:32173344..32173398,+p1@Rrp1b
Mm9::chr17:47748160..47748193,-p1@Bysl
Mm9::chr19:41970650..41970697,-p1@Rrp12
Mm9::chr19:46131044..46131076,+p1@Pprc1
Mm9::chr1:164478615..164478676,-p1@Mettl13
Mm9::chr1:9535478..9535560,+p1@Rrs1
Mm9::chr3:105762371..105762459,+p1@Wdr77
Mm9::chr3:129534207..129534259,-p2@Gar1
Mm9::chr4:120242857..120242904,-p1@Ctps
Mm9::chr4:151413424..151413465,+p1@Nol9
Mm9::chr4:155610108..155610159,+p@chr4:155610108..155610159
+
Mm9::chr4:45031491..45031547,+p1@Polr1e
Mm9::chr5:111082463..111082501,+p1@Ddx51
Mm9::chr5:120566489..120566534,+p1@Rbm19
Mm9::chr5:74489137..74489154,+p1@2700023E23Rik
Mm9::chr6:125081887..125081971,+p1@Nop2
Mm9::chr7:5013785..5013843,+p1@U2af2
Mm9::chr7:53086146..53086186,-p1@Grwd1
Mm9::chr8:90661743..90661801,+p1@Heatr3


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:0042254ribosome biogenesis and assembly5.11680186249144e-07
GO:0022613ribonucleoprotein complex biogenesis and assembly3.20675718272105e-06
GO:0005730nucleolus4.9783549932582e-06
GO:0016072rRNA metabolic process9.72423441477556e-06
GO:0006364rRNA processing9.72423441477556e-06
GO:0005634nucleus1.35386557805915e-05
GO:0003723RNA binding2.30020001477502e-05
GO:0006396RNA processing2.86814449429933e-05
GO:0016070RNA metabolic process0.00418132620189929
GO:0043231intracellular membrane-bound organelle0.00418132620189929
GO:0043227membrane-bound organelle0.00418132620189929
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0057915285466571
GO:0044428nuclear part0.0057915285466571
GO:0031981nuclear lumen0.00651548456133426
GO:0006996organelle organization and biogenesis0.00855697563088129
GO:0031974membrane-enclosed lumen0.00855697563088129
GO:0043233organelle lumen0.00855697563088129
GO:0010467gene expression0.00855697563088129
GO:0031074nucleocytoplasmic shuttling complex0.00855697563088129
GO:0042564NLS-dependent protein nuclear import complex0.00855697563088129
GO:0001651dense fibrillar component0.00855697563088129
GO:0003676nucleic acid binding0.00929918789864357
GO:0043229intracellular organelle0.0121978450728034
GO:0043226organelle0.0121978450728034
GO:0003883CTP synthase activity0.0138156121431303
GO:0030515snoRNA binding0.0138156121431303
GO:0000179rRNA (adenine-N6,N6-)-dimethyltransferase activity0.0179509488968946
GO:0016433rRNA (adenine) methyltransferase activity0.0179509488968946
GO:0008649rRNA methyltransferase activity0.0179509488968946
GO:0008026ATP-dependent helicase activity0.0181160658139124
GO:0000154rRNA modification0.0224270101912869
GO:0009303rRNA transcription0.0271701114396692
GO:0016779nucleotidyltransferase activity0.0285973935560174
GO:0004386helicase activity0.0388005106397328
GO:0016043cellular component organization and biogenesis0.0408817001251616



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><br><br>


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)
MA0003.10.136408
MA0004.13.68254
MA0006.11.77843
MA0007.10.319014
MA0009.10.412602
MA0014.10.377286
MA0017.10.0425137
MA0019.10.268299
MA0024.10.37648
MA0025.10.616209
MA0027.11.99083
MA0028.13.5596
MA0029.10.358857
MA0030.10.364159
MA0031.10.335674
MA0038.10.556221
MA0040.10.423075
MA0041.10.0680579
MA0042.10.0625496
MA0043.11.2388
MA0046.10.442826
MA0048.10.366277
MA0050.11.86378
MA0051.10.570537
MA0052.10.429851
MA0055.10.085769
MA0056.10
MA0057.10.0953992
MA0058.12.28588
MA0059.11.29681
MA0060.11.24013
MA0061.11.04677
MA0063.10
MA0066.10.182901
MA0067.10.717937
MA0068.10.10147
MA0069.10.430137
MA0070.10.421986
MA0071.10.393361
MA0072.10.414891
MA0073.10.00137944
MA0074.10.937227
MA0076.16.1517
MA0077.10.396883
MA0078.10.218627
MA0081.10.551199
MA0083.10.494326
MA0084.11.02883
MA0087.10.457205
MA0088.11.38927
MA0089.10
MA0090.10.0869074
MA0091.10.724669
MA0092.10.29369
MA0093.14.31452
MA0095.10
MA0098.10
MA0100.10.465083
MA0101.11.33732
MA0103.10.175527
MA0105.10.182808
MA0106.10.224053
MA0107.11.05433
MA0108.20.285422
MA0109.10
MA0111.10.644717
MA0113.11.11639
MA0114.10.0900443
MA0115.10.497446
MA0116.10.918929
MA0117.10.469566
MA0119.10.0688632
MA0122.10.486676
MA0124.10.668899
MA0125.10.601578
MA0130.10
MA0131.10.731896
MA0132.10
MA0133.10
MA0135.10.526836
MA0136.10.988731
MA0139.10.731715
MA0140.10.152839
MA0141.10.197414
MA0142.10.324241
MA0143.10.215799
MA0144.11.44299
MA0145.10.207994
MA0146.10.373398
MA0147.15.59323
MA0148.10.112635
MA0149.10.0709954
MA0062.28.01329
MA0035.20.472078
MA0039.22.23778
MA0138.20.259078
MA0002.20.284394
MA0137.23.36204
MA0104.24.03185
MA0047.20.18962
MA0112.21.20369
MA0065.20.115736
MA0150.10.318861
MA0151.10
MA0152.10.55517
MA0153.10.541494
MA0154.10.357361
MA0155.10.256374
MA0156.13.93316
MA0157.10.299365
MA0158.10
MA0159.10.805512
MA0160.10.739566
MA0161.10
MA0162.10.238334
MA0163.10.203588
MA0164.10.172802
MA0080.20.683908
MA0018.21.60801
MA0099.20.254459
MA0079.20.525161
MA0102.21.07954
MA0258.11.33284
MA0259.11.45352
MA0442.10
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