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MCL coexpression mm9:2272: Difference between revisions

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{{MCL_coexpression_mm9
{{MCL_coexpression_mm9|coexpression_dpi_cluster_scores_mean=-0.0945005916622382,-0.354315595367078,-0.450686473356945,-0.394949758686899,-0.359897603401284,-0.0976185590399629,-0.0875742115339554,-0.0473703194845318,0.47971245333593,0.512960644273904,0.484710256532012,0.480087856767474,-0.00354082999173042,-0.0140952159663562,0.0676573786633564,0.0957038014425002,0.0544836782852677,-0.0134959039503298,0.0164427052569493,-0.122087360793741,-0.124375646807859,0.0545022424942555,0.0990184887102728,-0.0815865268353373,-0.186319770030459,-0.349518164976354,-0.292446003715535,-0.172971229235324,-0.222528085307821,-0.138613410261369,-0.145105261673482,-0.0583170175733815,-0.0461982620576357,-0.0907480129030708,-0.110076191628711,-0.0753357852610645,-0.100509111010244,-0.374546123623057,-0.356094820182881,-0.339097559383072,-0.407822555673606,-0.471089799443301,-0.410112827283942,0.104636476930654,0.0754736571239264,0.0742378849129232,-0.649039565396368,-0.665307015915269,-0.802514596028749,-0.431687920464411,-0.578880607314404,-0.803164124439898,0.0234269418671788,-0.0285475236108516,0.0724698136394429,0.099584970993656,0.135287242882152,-0.0433204955486244,-0.395407605092441,-0.389159344001326,-0.402158524777553,-0.633010173355155,-0.642531152782128,-0.779793955589913,-0.718460568202883,-0.714845823216947,-0.734647059572364,-0.652827135973171,-0.226547139161655,-0.359480637575207,-0.31282783129977,-0.492096779192917,-0.413375771986208,-0.237571171435988,-0.388627530227396,-0.350299677228542,-0.113449313890035,-0.112629055131175,-0.0837026810716625,-0.399682938435475,-0.367527802292421,-0.271777117186857,-0.331236576311804,-0.232332243938259,-0.162743193159375,-0.0469300695688233,-0.00172523527034685,-0.133057231193286,0.1850113418596,0.106070832509519,-0.0504031528906471,-0.0645115166144315,-0.0109737581118103,0.0125975413293231,0.0548981886647444,0.085520864385102,0.0155086223579335,0.0963891129603026,-0.0673589382065111,-0.109829253505717,-0.159006349851415,0.0188948202784502,-0.104276038922261,-0.129760841158362,-0.0040945247393776,-0.0132074709633833,-0.0315471026975587,0.0163065478712756,0.322148765160098,0.00131006315594715,-0.0225448376763939,0.00955597554184943,-0.032281184315957,-0.04589594674,-0.00523666185583508,-0.115708378038222,-0.0139942396058864,0.101275010328597,0.0514624814108061,0.0359655696285778,0.0321943209277323,0.0619865018365104,-0.0433987732307355,-0.0441407339235027,-0.130758102200083,-0.0784900616200954,0.114094224506627,-0.0345638530719128,0.0723921932099905,-0.0618958313796287,0.0074301141220725,-0.0207446293019876,-0.0527726111055487,-0.0664714801170072,-0.0870646715817909,-0.088721809667723,-0.0224614622986297,-0.0212925686829132,-0.0109506429730844,-0.0068978788778387,0.0932423150079386,-0.0462187125406289,0.0459267302254967,0.0045097379998722,-0.0271564902033949,0.0344469083673301,-0.0737559546374663,-0.0121663755569523,0.0645635721754578,0.10481930983415,0.0729333942056199,0.0316203620897981,0.0807344463648794,0.097280977366754,0.0830185981590578,-0.0265618873416848,0.146949960621535,0.0928046335057092,0.0465002472767156,0.0605425461092939,0.0616937724432807,0.00531253792605212,0.0424139606750854,-0.0126665997241041,-0.0139161874341773,0.0103609823646525,-0.00469388078873657,-0.0122498713149535,-0.0439975489959876,-0.0511330652389041,0.00774988351673509,-0.0206823684965317,0.0353658278034285,-0.00130751807510743,-0.0255799061974486,0.0341831927647779,-0.308847254834484,0.0179824810285345,0.081178691954724,0.0803870320453576,0.104194228770912,0.0764739628623002,0.0371655170870448,-0.0375408440423301,-0.0836965819265158,-0.0264932576184772,-0.1132955126044,-0.105813441351345,-0.0543812703203501,0.0161346353783611,-0.0514979791139967,-0.0863050391014314,-0.295942448886235,0.0557898001749696,0.0337304687236342,0.0159756179968225,-0.00766972300585715,-0.0316107271120088,-0.046178955941463,0.0101841540781856,-0.0146123253656031,-0.0565879988380227,0.0512467238359852,0.2067548844653,0.20467665548705,0.19668644115232,0.163842569720772,0.10980269577977,0.0354156950941161,0.0659517762501759,0.103389483675321,0.0664524401146775,0.14388715291952,0.0376627420878402,0.07011916020014,0.102138579962068,0.137103463392713,0.105378795077346,-0.0429597324205783,0.0271967077422181,0.107561392788933,0.0488249591925886,-0.00239222595168695,-0.0172683479240349,-0.0439480023624283,-0.107222833741027,0.0132551911499556,-0.0616003062566555,-0.0593745273672387,-0.0890971284349781,-0.0836459600893826,-0.138635766337532,-0.211978312762407,-0.117186702937363,0.199991883306184,0.185740040525818,-0.0205201525581477,-0.0786407479296151,0.250009474817902,0.129796767620282,-0.0143104777700202,0.0252383391429971,-0.00420795655401383,0.0181898939036716,-0.0087865298988497,-0.0114474321315895,0.00838783067796043,-0.0245792191232936,0.00786027474941738,-0.0358333826619006,0.0302383814349225,-0.154257341046695,-0.0245665884053393,0.00834083116593993,0.276278662579149,0.0543146858467494,0.0461874388850697,0.182499325849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gostat_on_MCL_coexpression=GO:0006412;translation;0.00376893364516052;56347,107508!GO:0003743;translation initiation factor activity;0.00376893364516052;56347!GO:0009059;macromolecule biosynthetic process;0.00376893364516052;56347,107508!GO:0008135;translation factor activity, nucleic acid binding;0.00376893364516052;56347!GO:0044249;cellular biosynthetic process;0.00376893364516052;56347,107508!GO:0005852;eukaryotic translation initiation factor 3 complex;0.00376893364516052;56347!GO:0004827;proline-tRNA ligase activity;0.00376893364516052;107508!GO:0006433;prolyl-tRNA aminoacylation;0.00376893364516052;107508!GO:0006424;glutamyl-tRNA aminoacylation;0.00376893364516052;107508!GO:0004818;glutamate-tRNA ligase activity;0.00376893364516052;107508!GO:0043022;ribosome binding;0.00660666148335938;56347!GO:0009058;biosynthetic process;0.00660666148335938;56347,107508!GO:0043021;ribonucleoprotein binding;0.0231667648280763;56347!GO:0051536;iron-sulfur cluster binding;0.0376124820187361;24015!GO:0051540;metal cluster binding;0.0376124820187361;24015!GO:0006413;translational initiation;0.0376124820187361;56347!GO:0043038;amino acid activation;0.0376124820187361;107508!GO:0043039;tRNA aminoacylation;0.0376124820187361;107508!GO:0006418;tRNA aminoacylation for protein translation;0.0376124820187361;107508!GO:0044267;cellular protein metabolic process;0.0376124820187361;56347,107508!GO:0016875;ligase activity, forming carbon-oxygen bonds;0.0376124820187361;107508!GO:0016876;ligase activity, forming aminoacyl-tRNA and related compounds;0.0376124820187361;107508!GO:0004812;aminoacyl-tRNA ligase activity;0.0376124820187361;107508!GO:0044260;cellular macromolecule metabolic process;0.0376124820187361;56347,107508!GO:0010467;gene expression;0.0376124820187361;56347,107508!GO:0019538;protein metabolic process;0.0386103724222805;56347,107508!GO:0022618;protein-RNA complex 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|gostat_on_MCL_coexpression=GO:0006412;translation;0.00376893364516052;56347,107508!GO:0003743;translation initiation factor activity;0.00376893364516052;56347!GO:0009059;macromolecule biosynthetic process;0.00376893364516052;56347,107508!GO:0008135;translation factor activity, nucleic acid binding;0.00376893364516052;56347!GO:0044249;cellular biosynthetic process;0.00376893364516052;56347,107508!GO:0005852;eukaryotic translation initiation factor 3 complex;0.00376893364516052;56347!GO:0004827;proline-tRNA ligase activity;0.00376893364516052;107508!GO:0006433;prolyl-tRNA aminoacylation;0.00376893364516052;107508!GO:0006424;glutamyl-tRNA aminoacylation;0.00376893364516052;107508!GO:0004818;glutamate-tRNA ligase activity;0.00376893364516052;107508!GO:0043022;ribosome binding;0.00660666148335938;56347!GO:0009058;biosynthetic process;0.00660666148335938;56347,107508!GO:0043021;ribonucleoprotein binding;0.0231667648280763;56347!GO:0051536;iron-sulfur cluster binding;0.0376124820187361;24015!GO:0051540;metal cluster binding;0.0376124820187361;24015!GO:0006413;translational initiation;0.0376124820187361;56347!GO:0043038;amino acid activation;0.0376124820187361;107508!GO:0043039;tRNA aminoacylation;0.0376124820187361;107508!GO:0006418;tRNA aminoacylation for protein translation;0.0376124820187361;107508!GO:0044267;cellular protein metabolic process;0.0376124820187361;56347,107508!GO:0016875;ligase activity, forming carbon-oxygen bonds;0.0376124820187361;107508!GO:0016876;ligase activity, forming aminoacyl-tRNA and related compounds;0.0376124820187361;107508!GO:0004812;aminoacyl-tRNA ligase activity;0.0376124820187361;107508!GO:0044260;cellular macromolecule metabolic process;0.0376124820187361;56347,107508!GO:0010467;gene expression;0.0376124820187361;56347,107508!GO:0019538;protein metabolic process;0.0386103724222805;56347,107508!GO:0022618;protein-RNA complex assembly;0.0485841810583763;56347!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000475!3.31e-11!150;UBERON:0002075!8.14e-08!19;UBERON:0000949!8.69e-08!72;UBERON:0003102!1.94e-07!22;UBERON:0001041!2.65e-07!80;UBERON:0002365!3.98e-07!25;UBERON:0002330!3.98e-07!25;UBERON:0001264!8.25e-07!12
}}

Latest revision as of 18:16, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr19:60866520..60866575,-p1@Eif3a
Mm9::chr1:187186955..187187029,+p1@Eprs
p1@LOC100504962
Mm9::chr7:133709878..133709930,-p1@Eif3c
Mm9::chr8:82235530..82235594,-p1@Abce1


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:0006412translation0.00376893364516052
GO:0003743translation initiation factor activity0.00376893364516052
GO:0009059macromolecule biosynthetic process0.00376893364516052
GO:0008135translation factor activity, nucleic acid binding0.00376893364516052
GO:0044249cellular biosynthetic process0.00376893364516052
GO:0005852eukaryotic translation initiation factor 3 complex0.00376893364516052
GO:0004827proline-tRNA ligase activity0.00376893364516052
GO:0006433prolyl-tRNA aminoacylation0.00376893364516052
GO:0006424glutamyl-tRNA aminoacylation0.00376893364516052
GO:0004818glutamate-tRNA ligase activity0.00376893364516052
GO:0043022ribosome binding0.00660666148335938
GO:0009058biosynthetic process0.00660666148335938
GO:0043021ribonucleoprotein binding0.0231667648280763
GO:0051536iron-sulfur cluster binding0.0376124820187361
GO:0051540metal cluster binding0.0376124820187361
GO:0006413translational initiation0.0376124820187361
GO:0043038amino acid activation0.0376124820187361
GO:0043039tRNA aminoacylation0.0376124820187361
GO:0006418tRNA aminoacylation for protein translation0.0376124820187361
GO:0044267cellular protein metabolic process0.0376124820187361
GO:0016875ligase activity, forming carbon-oxygen bonds0.0376124820187361
GO:0016876ligase activity, forming aminoacyl-tRNA and related compounds0.0376124820187361
GO:0004812aminoacyl-tRNA ligase activity0.0376124820187361
GO:0044260cellular macromolecule metabolic process0.0376124820187361
GO:0010467gene expression0.0376124820187361
GO:0019538protein metabolic process0.0386103724222805
GO:0022618protein-RNA complex assembly0.0485841810583763



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
organism subdivision3.31e-11150
viscus8.14e-0819
endocrine system8.69e-0872
surface structure1.94e-0722
foregut2.65e-0780
exocrine gland3.98e-0725
exocrine system3.98e-0725
pancreas8.25e-0712


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)
MA0003.10.331308
MA0004.10.6888
MA0006.11.24418
MA0007.10.672186
MA0009.11.15569
MA0014.10.581929
MA0017.10.528196
MA0019.10.964875
MA0024.11.11019
MA0025.11.39562
MA0027.12.81824
MA0028.11.26991
MA0029.11.08753
MA0030.11.09438
MA0031.11.05719
MA0038.10.846479
MA0040.11.16866
MA0041.10.604221
MA0042.10.589368
MA0043.11.25564
MA0046.11.1929
MA0048.10.266382
MA0050.10.731539
MA0051.10.856094
MA0052.11.17701
MA0055.10.396346
MA0056.10
MA0057.10.251896
MA0058.11.4226
MA0059.11.45189
MA0060.10.403071
MA0061.10.438628
MA0063.10
MA0066.10.834648
MA0067.11.50873
MA0068.10.256913
MA0069.11.17737
MA0070.11.16732
MA0071.10.73062
MA0072.11.15853
MA0073.10.0471131
MA0074.10.795862
MA0076.11.35592
MA0077.11.13603
MA0078.10.891476
MA0081.10.621611
MA0083.11.25482
MA0084.11.84013
MA0087.11.21037
MA0088.10.582815
MA0089.10
MA0090.10.650768
MA0091.10.703314
MA0092.10.651119
MA0093.11.29026
MA0095.10
MA0098.10
MA0100.10.783305
MA0101.10.605676
MA0103.10.540576
MA0105.10.313353
MA0106.10.899777
MA0107.10.533522
MA0108.20.989014
MA0109.10
MA0111.10.666525
MA0113.10.869608
MA0114.11.11164
MA0115.11.25852
MA0116.10.497293
MA0117.11.22527
MA0119.10.606338
MA0122.11.24573
MA0124.11.45461
MA0125.11.37907
MA0130.10
MA0131.10.960068
MA0132.10
MA0133.10
MA0135.11.29308
MA0136.10.817395
MA0139.10.365453
MA0140.10.78318
MA0141.10.563066
MA0142.11.04199
MA0143.10.887119
MA0144.11.95888
MA0145.10.21199
MA0146.10.647546
MA0147.11.15069
MA0148.10.706718
MA0149.10.611881
MA0062.21.54479
MA0035.20.788288
MA0039.20.0959929
MA0138.20.951653
MA0002.20.368961
MA0137.20.559766
MA0104.21.77707
MA0047.20.845655
MA0112.20.608441
MA0065.21.14711
MA0150.10.67206
MA0151.10
MA0152.10.84577
MA0153.11.31015
MA0154.10.263609
MA0155.10.650923
MA0156.10.549102
MA0157.11.0083
MA0158.10
MA0159.10.465802
MA0160.10.71003
MA0161.10
MA0162.10.346529
MA0163.11.11502
MA0164.10.817786
MA0080.20.534538
MA0018.21.93488
MA0099.20.944966
MA0079.20.0553806
MA0102.21.8929
MA0258.10.419871
MA0259.11.12353
MA0442.10
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