search for: enriched

Hi, I used GOstats to perform enrichment test on a set of genes (20). There are 7 GO terms with pvalue less than cuttoff and therefore shown in the result table. How can I get the information that which gene in the input gene set belong to which GO term of these enriched GO terms? Thanks for any comments. best, Tim [[alternative HTML version deleted]]

...Analysis). By utilizing the interaction information, the tool identifies most of the involved pathways. pathfindR also creates pathway diagrams with the involved genes colored by change values. (this is achieved using the bioconductor package pathview) Finally, the package allows for clustering of enriched pathways and establishment of representative pathways. This allows for further abstraction and reduces the complexity of analysis. You can read more about the package and a case study in our pre-print <https://doi.org/10.1101/272450> [[alternative HTML version deleted]] ____________________...

...Analysis). By utilizing the interaction information, the tool identifies most of the involved pathways. pathfindR also creates pathway diagrams with the involved genes colored by change values. (this is achieved using the bioconductor package pathview) Finally, the package allows for clustering of enriched pathways and establishment of representative pathways. This allows for further abstraction and reduces the complexity of analysis. You can read more about the package and a case study in our pre-print <https://doi.org/10.1101/272450> [[alternative HTML version deleted]] ____________________...

Hi List I have data in the following form: Gene    TFBS NUDC     PPARA(1) HNF4(20) HNF4(96) AHRARNT(104) CACBINDINGPROTEIN(149) T3R(167) HLF(191) RPA2     STAT4(57) HEB(251) TAF12     PAX3(53) YY1(92) BRCA(99) GLI(101) EIF3I     NERF(10) P300(10) TRAPPC3     HIC1(3) PAX5(17) PAX5(110) NRF1(119) HIC1(122) TRAPPC3     EGR(26) ZNF219(27) SP3(32) EGR(32) NFKAPPAB65(89) NFKAPPAB(89) RFX(121)

Dear R users,  I hope you can help me as you have done before.  I was wondering if I can make some of the points on my graph a different colour and symbol? Some of my soil samples are enriched and I wanted them to be shown with a red triangle and the samples which are not enriched I wanted to show with a blue square. I can't seem to find a way of doing this if there is a way?  My script:            x <- c(0, 50, 100, 250, 500, 750, 1000, 1500, 2000, 2500, 3000)            y <...

...+4)],collapse="") } > ADDRESSES [1] "14265" "42650" "265011" "6501110" "5011104" "0111043" "1110436" "104368" [9] "43686" Atte Tenkanen University of Turku, Finland [[alternative text/enriched version deleted]]

I'm having problems with this example, it is posted with reproduceable code below, both with the normal 0-6 scale and the desired 3-6 scale (with bars removed). How can I get the graph to have the desired 3-6 scale without removing the bars. Thanks! #Data

Hi, I am very new to R and wanted to know if there is a package that, given very long nucleotide sequences, searches and identifies short (7-10nt) motifs.. I would like to look for enrichment of certain motifs in genomic sequences. I tried using MEME (not an R package, I know), but the online version only allows sequences up to MAX 60000 nucleotides, and that's too short for my needs..

...x = 5) levelplot(var1.pred~x+y, k, aspect = mapasp(k), main = "Predicted 5m") It executes fine (it plots up) when I cut and paste to the command prompt but it seems to be missed (nothing occurs) when I call the source file. I am using OSX. Thanks for any help. Matt [[alternative text/enriched version deleted]]

Hi all, I'm discovering LLVM and I want to build a customized CFG with customized nodes (here BasicBlocks). Simply, the purpose is to enrich CFG with some other informations. What is the best way to do that ? Please, tell me if I'm wrong (I'm not familiar enough with c++) but I understand that : - CFG is a GraphTraits<BasicBlock*> - it's not allowed to inherit from

...rginia Department of Psychology USPS: P.O.Box 400400 Charlottesville, VA 22904-4400 Parcels: Room 102 Gilmer Hall McCormick Road Charlottesville, VA 22903 Office: B011 +1-434-982-4729 Lab: B019 +1-434-982-4751 Fax: +1-434-982-4766 WWW: http://www.people.virginia.edu/~mk9y/ [[alternative text/enriched version deleted]]

Dear All, I need to fetch GO ontologies for Homo sapiens with their mappings to corresponding Uniprot identifiers. I would be using this information to compare result from a clustering algorithm with existing protein complexes. This would be a test to check how the clustering algorithm accurately captures GO terms with respect to the known protein complexes. Can anyone suggest a simple workflow

...ion? (or is that too slow?) Many Thanks in Advance! Mike Mike Hickerson University of California Museum of Vertebrate Zoology 3101 Valley Life Sciences Building Berkeley, California  94720-3160  USA voice 510-642-8911 cell: 510-701-0861 fax 510-643-8238 mhick@berkeley.edu [[alternative text/enriched version deleted]]

...e$Day,frame$Time),mean) Group.1 Group.2 Time V1 V2 1 M 0 0 4.000000 2 2 T 0 0 4.000000 45 3 M 1 1 10 5 4 T 1 1 4.333333 2 > I hope my description makes sense and appreciate any help. Yours Frank [[alternative text/enriched version deleted]]

For example, this station: http://radio.dyne.org:8000/ondarossa.mp3 has got a xspf file? I obtain a message: Could not parse XSLT file when i try to open it For the stations that I can't found in yp.xml (e.g. http://212.162.68.230/1.mp3 http://212.162.68.230/2.mp3 http://212.162.68.230/3.mp3 http://stream15.top-ix.org/ondequadre ) it means they aren't on an official

Hi in order to keep the dial tone after pressing 9 for 'outside line' I have this in my extensions.conf [localpstn] ignorepat => 9 exten => _9[123456789]XXXXXXX,1,Dial,${PSTN}/${EXTEN:1} exten => _9[123456789]XXXXXXX,2,Congestion this is properly included in the handsets' context but the dial tone disappears after pressing 9. am I missing something? thanks in advance

Hi John, thank you for your answer. Sorry if I was not clear ^^' I try to build a RCG (Resource Control Graph) which is a CFG with a weight. In my case, this weight corresponds to the number of heap allocations. Then I want to add this weight to each node (then basic block) of this graph. I think that a CFG is a GraphTraits<BasicBlock*> then I suppose that this RCG will be a

...ficial page: Go to the list page : http://www.stat.math.ethz.ch/mailman/listinfo/r-sig-mac To post a message to this list just send a mail to r-sig- mac at stat.math.ethz.ch Stefano -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 819 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-announce/attachments/20010428/f43a25e6/attachment.bin>

A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1168 bytes Desc: not available Url : https://stat.ethz.ch/pipermail/r-help/attachments/20010119/d640fae5/attachment.bin

Hi, Has anyone written code for isotonic regression on ordered rectangular grids? Nathan Nathan Leon Pace, MD, MStat University of Utah Salt Lake City, UT 84132 Office: 801.581.6393 Fax: 801.581.4367 Cell: 801.558.3987 Pager: 801.291.9019 Home: 801.467.2925 [[alternative text/enriched version deleted]]