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MCL coexpression mm9:327: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0005634;nucleus;0.00893147018551157;71041,231452,21815,70428,17975,71991,26939,11834,28036,53319,245000,67628!GO:0044424;intracellular part;0.00893147018551157;71041,12469,231452,21815,70428,17975,13627,24030,67738,71991,26939,11834,28036,53319,245000,67628,72831!GO:0003723;RNA binding;0.00893147018551157;28036,11834,53319,17975,72831!GO:0005622;intracellular;0.00893147018551157;71041,12469,231452,21815,70428,17975,13627,24030,67738,71991,26939,11834,28036,53319,245000,67628,72831!GO:0043231;intracellular membrane-bound organelle;0.00893147018551157;71041,231452,21815,70428,17975,24030,71991,26939,11834,28036,53319,245000,67628,72831!GO:0043227;membrane-bound organelle;0.00893147018551157;71041,231452,21815,70428,17975,24030,71991,26939,11834,28036,53319,245000,67628,72831!GO:0010467;gene expression;0.0124184894000314;71041,21815,70428,13627,24030,71991,11834,28036,26939!GO:0003676;nucleic acid binding;0.0124184894000314;21815,70428,17975,13627,11834,28036,53319,245000,72831!GO:0003899;DNA-directed RNA polymerase activity;0.0124184894000314;26939,70428!GO:0000166;nucleotide binding;0.0250303259944819;13627,12469,28036,53319,57815,17975,72831!GO:0043229;intracellular organelle;0.0250303259944819;71041,231452,21815,70428,17975,24030,71991,26939,11834,28036,53319,245000,67628,72831!GO:0043226;organelle;0.0250303259944819;71041,231452,21815,70428,17975,24030,71991,26939,11834,28036,53319,245000,67628,72831!GO:0032405;MutLalpha complex binding;0.0250303259944819;245000!GO:0032407;MutSalpha complex binding;0.0250303259944819;245000!GO:0008432;JUN kinase binding;0.0250303259944819;21815!GO:0032404;mismatch repair complex binding;0.0250303259944819;245000!GO:0042405;nuclear inclusion body;0.0250303259944819;53319!GO:0044428;nuclear part;0.0250303259944819;71991,21815,11834,53319,17975!GO:0000109;nucleotide-excision repair complex;0.034379028864868;71991!GO:0016973;poly(A)+ mRNA export from nucleus;0.0395695407995545;53319!GO:0006283;transcription-coupled nucleotide-excision repair;0.0395695407995545;71991!GO:0016234;inclusion body;0.0395695407995545;53319!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.040060873560071;71041,21815,70428,71991,11834,28036,26939,245000!GO:0016779;nucleotidyltransferase activity;0.0418329151080293;26939,70428!GO:0005528;FK506 binding;0.0418329151080293;67738!GO:0005527;macrolide binding;0.0418329151080293;67738!GO:0043393;regulation of protein binding;0.0464582033755782;245000!GO:0008144;drug binding;0.0464582033755782;67738!GO:0044238;primary metabolic process;0.0464582033755782;71041,12469,21815,70428,13627,24030,67738,71991,11834,28036,26939,245000!GO:0051320;S phase;0.0464582033755782;67628!GO:0000084;S phase of mitotic cell cycle;0.0464582033755782;67628!GO:0044237;cellular metabolic process;0.0464582033755782;71041,12469,21815,70428,13627,24030,67738,71991,11834,28036,26939,245000!GO:0006457;protein folding;0.0464582033755782;12469,67738!GO:0005487;nucleocytoplasmic transporter activity;0.0496520151209464;53319!}}
{{MCL_coexpression_mm9
|coexpression_dpi_cluster_scores_mean=0.0433114719131853,-0.258560109592974,-0.301941388495981,-0.357128914224878,-0.297057212489734,-0.0485084718128483,-0.0438670704255256,0.175278848264284,0.806862436765576,0.866030943515429,0.686580384581768,0.672929593201422,0.172896993866176,0.184713947773988,0.0929345979950239,0.13828475534366,0.0409591562133633,0.160135118429756,0.13392966275404,0.0860912000433366,0.296035910977692,0.118929944411705,0.174893452794645,-0.084043602840167,-0.0931790268425613,-0.334142430264525,-0.264854117118878,-0.153693176601067,-0.190879533873696,-0.140809787110452,-0.0881704627934885,0.271646155711748,0.267132153497816,-0.254089377881557,0.0490789127469482,0.01338020983171,0.0610825905166753,-0.30623022708479,-0.248658563000514,-0.225797681967665,-0.327720231838962,-0.427063415955338,-0.281926019064585,-0.0133337353181893,-0.0392866203825084,-0.00989441831394722,-0.313629905615758,-0.270538971406676,-0.323573979988974,-0.237092039075074,-0.236196413137582,-0.343270610138962,0.221369565135049,0.180849146775496,0.191095810318046,-0.124507490249825,-0.150562073843373,-0.162367916652175,-0.0012740673054122,0.0088476987307676,-0.0225824979200693,-0.257191950038928,-0.374005429294754,-0.309411677854343,-0.26228273705011,-0.327145717536544,-0.301842701681273,-0.28309744531077,-0.0146796348448133,-0.03798153613775,-0.0342610774354709,-0.129133892314513,-0.108740955355399,-0.0122566176692694,-0.0123319610579443,-0.0621085522671263,-0.134449367831845,-0.0408868428439604,-0.0258867327261283,-0.00517631120393769,0.00778384456916058,0.021311096578187,-0.0752120737788998,-0.0872516276015393,-0.0486828868394264,-0.00835465647075928,-0.0128284770704827,0.0202416304075254,0.131824619816664,-0.0314551389364008,0.0269474618360405,-0.141432772510965,0.0467387188843199,-0.196742991978861,-0.177064034256232,-0.158290230412835,-0.0457372350578811,-0.0899675191152765,-0.130969737287651,-0.127017752415266,-0.0237696780153391,-0.166797237771924,-0.156283844664593,-0.34101079479832,-0.0271555126989669,-0.0258365452678173,-0.0430978751841077,-0.0176495417344043,0.212339449546248,-0.0403725579886048,0.0438440127180619,0.00866252792033829,-0.0360623202751918,-0.026077933877267,0.00424045305129403,-0.108514303615973,-0.0239289962357727,-0.10301223547353,-0.00212481815405386,-0.00105479850874789,-0.0199773238475023,0.0264388043369638,-0.244903438661576,0.0372386372974797,-0.0124706972298456,-0.120780617835191,0.221139492767758,0.151335433587407,0.199759532309895,0.0348020963204848,0.0231972750400368,0.040618438783909,0.0166643866617162,0.0393682823894778,-0.0162680466224601,-0.00575565333270708,0.0194524836008314,-0.0258910301210417,-0.0312895001719456,-0.117106215970536,0.178845333955476,0.0933862334020729,0.0855139897449045,0.0609511200426191,0.0786037980036143,0.0841258265994195,0.0598465307105126,-0.00191118017255739,0.167268151077282,0.163859217793823,0.136298530174938,0.0845003334924605,0.0718727451756734,0.017174090506948,0.00973973652045143,0.127209883944473,0.267604506022016,0.211211858558707,0.14618069763247,0.0900289056181246,0.0814221210265181,0.0563742803778788,-0.017955250154555,-0.0344247877480119,-0.0193502076010253,-0.037798283124563,-0.0514490737019804,-0.0375487769986182,-0.061513204128444,-0.0613894556434745,-0.140015322043202,-0.141170902015741,-0.0891174911615915,-0.15823004151309,-0.00109970119233919,0.0745891392150798,-0.303822229048637,-0.07334815726261,0.145939781116575,0.127861139495761,0.0979333949869185,0.0379012847333712,-0.0237553643148852,-0.065339073673572,-0.17642469998399,-0.0897015670765564,-0.086808382579753,-0.0785472178631661,-0.0703874993217713,-0.170795060608594,-0.114474075294558,-0.141789820637774,0.0744953378565834,0.128509231743404,0.0476053752995809,0.0587267557914969,0.043331040254513,0.0380861414871364,-0.0142033137766052,-0.0635792716535992,-0.0936318868648818,-0.0966476987309533,-0.06610022690644,0.199430150084981,0.188055403395066,0.160894406994655,0.0908285787887595,0.0811536221429299,0.0369025544191611,0.014936025587925,0.0370822926300547,0.00852936365873662,-0.0907127207333912,-0.0781017783047126,-0.0691876218055869,-0.119252641711935,-0.122534435017384,-0.12659919850014,-0.0719015142974607,0.119633050932348,0.137085590162879,0.099782392338006,0.0477942098557901,0.0128162164573034,-0.0519581109321161,-0.0373637965178631,-0.0146376791590364,-0.0465316807308486,-0.0834091547864204,-0.106270489879623,-0.122932445743327,-0.133372338865531,-0.0448991568262092,-0.0850061278232991,-0.0717340611409192,-0.0325947051127461,-0.0253956708434687,-0.00858297803283477,0.051706927508376,-0.125622423267922,0.0802092688145551,0.0365976286726493,0.0256874449627168,0.059041789772464,0.0491696916186881,0.0288997143375195,0.085020845517466,0.00456462348811124,0.0409420467783353,0.0146264074564758,0.0336037318770729,0.00620390599089641,0.0682898626955515,0.0454982207562821,-0.0280776835035064,0.0820409799277795,0.0211039390926928,-0.039590126666947,-0.0764200511761377,-0.004401982803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|gostat_on_MCL_coexpression=GO:0005634;nucleus;0.00893147018551157;71041,231452,21815,70428,17975,71991,26939,11834,28036,53319,245000,67628!GO:0044424;intracellular part;0.00893147018551157;71041,12469,231452,21815,70428,17975,13627,24030,67738,71991,26939,11834,28036,53319,245000,67628,72831!GO:0003723;RNA binding;0.00893147018551157;28036,11834,53319,17975,72831!GO:0005622;intracellular;0.00893147018551157;71041,12469,231452,21815,70428,17975,13627,24030,67738,71991,26939,11834,28036,53319,245000,67628,72831!GO:0043231;intracellular membrane-bound organelle;0.00893147018551157;71041,231452,21815,70428,17975,24030,71991,26939,11834,28036,53319,245000,67628,72831!GO:0043227;membrane-bound organelle;0.00893147018551157;71041,231452,21815,70428,17975,24030,71991,26939,11834,28036,53319,245000,67628,72831!GO:0010467;gene expression;0.0124184894000314;71041,21815,70428,13627,24030,71991,11834,28036,26939!GO:0003676;nucleic acid binding;0.0124184894000314;21815,70428,17975,13627,11834,28036,53319,245000,72831!GO:0003899;DNA-directed RNA polymerase activity;0.0124184894000314;26939,70428!GO:0000166;nucleotide binding;0.0250303259944819;13627,12469,28036,53319,57815,17975,72831!GO:0043229;intracellular organelle;0.0250303259944819;71041,231452,21815,70428,17975,24030,71991,26939,11834,28036,53319,245000,67628,72831!GO:0043226;organelle;0.0250303259944819;71041,231452,21815,70428,17975,24030,71991,26939,11834,28036,53319,245000,67628,72831!GO:0032405;MutLalpha complex binding;0.0250303259944819;245000!GO:0032407;MutSalpha complex binding;0.0250303259944819;245000!GO:0008432;JUN kinase binding;0.0250303259944819;21815!GO:0032404;mismatch repair complex binding;0.0250303259944819;245000!GO:0042405;nuclear inclusion body;0.0250303259944819;53319!GO:0044428;nuclear part;0.0250303259944819;71991,21815,11834,53319,17975!GO:0000109;nucleotide-excision repair complex;0.034379028864868;71991!GO:0016973;poly(A)+ mRNA export from nucleus;0.0395695407995545;53319!GO:0006283;transcription-coupled nucleotide-excision repair;0.0395695407995545;71991!GO:0016234;inclusion body;0.0395695407995545;53319!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.040060873560071;71041,21815,70428,71991,11834,28036,26939,245000!GO:0016779;nucleotidyltransferase activity;0.0418329151080293;26939,70428!GO:0005528;FK506 binding;0.0418329151080293;67738!GO:0005527;macrolide binding;0.0418329151080293;67738!GO:0043393;regulation of protein binding;0.0464582033755782;245000!GO:0008144;drug binding;0.0464582033755782;67738!GO:0044238;primary metabolic process;0.0464582033755782;71041,12469,21815,70428,13627,24030,67738,71991,11834,28036,26939,245000!GO:0051320;S phase;0.0464582033755782;67628!GO:0000084;S phase of mitotic cell cycle;0.0464582033755782;67628!GO:0044237;cellular metabolic process;0.0464582033755782;71041,12469,21815,70428,13627,24030,67738,71991,11834,28036,26939,245000!GO:0006457;protein folding;0.0464582033755782;12469,67738!GO:0005487;nucleocytoplasmic transporter activity;0.0496520151209464;53319!
}}

Revision as of 11:07, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:23506949..23506966,-p4@Gm10279
p4@Gm14059
p4@Gm14958
p4@Gm5642
p4@Gm6646
p4@Gm7643
p4@Gm7671
p4@Gm7698
p4@Gm7711
p4@Rps12
Mm9::chr10:84085110..84085155,+p1@Polr3b
Mm9::chr13:108948917..108948948,+p1@Ercc8
Mm9::chr16:87496052..87496065,-p2@Cct8
Mm9::chr16:90810610..90810674,-p1@Urb1
Mm9::chr17:71202822..71202877,-p3@Tgif1
Mm9::chr19:47125313..47125405,-p1@Pcgf6
Mm9::chr19:8831589..8831616,+p2@Nxf1
Mm9::chr1:88256056..88256061,-p2@Ncl
Mm9::chr2:114001010..114001029,-p3@Aqr
Mm9::chr3:127256128..127256143,-p2@Larp7
Mm9::chr3:157694612..157694655,-p5@Srsf11
Mm9::chr3:37319195..37319257,+p1@Spata5
Mm9::chr3:79395359..79395370,+p2@Ppid
Mm9::chr4:135412002..135412039,+p2@Srsf10
Mm9::chr4:46463743..46463759,+p3@Anp32b
Mm9::chr5:121847974..121848013,+p1@Naa25
Mm9::chr5:92738974..92739026,-p1@Sdad1
Mm9::chr7:128061283..128061329,+p1@Polr3e
Mm9::chr7:133645494..133645563,-p@chr7:133645494..133645563
-
Mm9::chr8:126545352..126545415,+p1@Urb2
Mm9::chr9:110003514..110003556,-p2@Dhx30
Mm9::chr9:78329464..78329521,-p1@Eef1a1
Mm9::chr9:95758113..95758129,+p2@Atr


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:0005634nucleus0.00893147018551157
GO:0044424intracellular part0.00893147018551157
GO:0003723RNA binding0.00893147018551157
GO:0005622intracellular0.00893147018551157
GO:0043231intracellular membrane-bound organelle0.00893147018551157
GO:0043227membrane-bound organelle0.00893147018551157
GO:0010467gene expression0.0124184894000314
GO:0003676nucleic acid binding0.0124184894000314
GO:0003899DNA-directed RNA polymerase activity0.0124184894000314
GO:0000166nucleotide binding0.0250303259944819
GO:0043229intracellular organelle0.0250303259944819
GO:0043226organelle0.0250303259944819
GO:0032405MutLalpha complex binding0.0250303259944819
GO:0032407MutSalpha complex binding0.0250303259944819
GO:0008432JUN kinase binding0.0250303259944819
GO:0032404mismatch repair complex binding0.0250303259944819
GO:0042405nuclear inclusion body0.0250303259944819
GO:0044428nuclear part0.0250303259944819
GO:0000109nucleotide-excision repair complex0.034379028864868
GO:0016973poly(A)+ mRNA export from nucleus0.0395695407995545
GO:0006283transcription-coupled nucleotide-excision repair0.0395695407995545
GO:0016234inclusion body0.0395695407995545
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.040060873560071
GO:0016779nucleotidyltransferase activity0.0418329151080293
GO:0005528FK506 binding0.0418329151080293
GO:0005527macrolide binding0.0418329151080293
GO:0043393regulation of protein binding0.0464582033755782
GO:0008144drug binding0.0464582033755782
GO:0044238primary metabolic process0.0464582033755782
GO:0051320S phase0.0464582033755782
GO:0000084S phase of mitotic cell cycle0.0464582033755782
GO:0044237cellular metabolic process0.0464582033755782
GO:0006457protein folding0.0464582033755782
GO:0005487nucleocytoplasmic transporter activity0.0496520151209464



Relative expression of the co-expression cluster over median <br>Analyst:


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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>disease_data<br>

Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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)

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