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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



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


"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.

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)

{{{tfbs_overrepresentation_jaspar}}}

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