Hi Vincent, Thank you for your response. Just letting you know that your advice was very useful and that with a few minor adjustments I was able to perform a similar analysis to that I had performed using the KEGG pathways. -Paul. On Wed, Jan 21, 2009 at 4:00 PM, Vincent Carey <stvjc at="" channing.harvard.edu=""> wrote: > > On Wed, Jan 21, 2009 at 6:56 AM, Paul Geeleher <paulgeeleher at="" gmail.com=""> > wrote: >> >> Hi All, >> >> I've been following the instructions here: >> >> >> http://www.bioconductor.org/workshops/2007/seattle_bioc_intro_nov_0 7/folder.2007-11-30.5595085375/ >> >> to find dysregulated kegg pathways in a dataset. What I'm now >> wondering is if I can use the same methodology to find co-regulated >> genes / genes with common transcription factors? >> >> I'd assume its simply of redefining the gene set >> >> gsc <- GeneSetCollection(eset, setType = KEGGCollection()) >> to >> gsc <- GeneSetCollection(eset, setType = >> CoRegulatedGenesOrSomeFunctionLikeThat()) >> >> >> I suppose what I'm asking is if such a gene set exists in >> Bioconductor? And if not can this be done somewhere else? > > GSEABase has infrastructure to import the Broad MSIGDB from its XML > serialization; > see http://www.broad.mit.edu/gsea/downloads.jsp, where you will need to > register. > > If you use getBroadSets() in GSEABase to import the entire MSIGDB you will > have access to > 5452 gene sets. Broad categorizes these in five groups; group c3 includes > motif gene sets > which includes a subclass called transcription factor targets. > > Digging through a GSEABase GeneSetCollection can proceed in various ways. > What I will > show is probably not the most elegant approach: > > Assume you have imported the whole MSIGDB as msig2.5 > >> isC3 = which(sapply(msig2.5, function(x)bcCategory(collectionType(x))) == >> "c3") >> C3coll = msig2.5[isC3] >> C3coll > GeneSetCollection > names: RGAGGAARY_V$PU1_Q6, KRCTCNNNNMANAGC_UNKNOWN, ..., GTTATAT,MIR-410 > (837 total) > unique identifiers: PCDHGA5, CTXL, ..., pp9099 (15718 total) > types in collection: > geneIdType: SymbolIdentifier (1 total) > collectionType: BroadCollection (1 total) >> C3coll[[1]] > setName: RGAGGAARY_V$PU1_Q6 > geneIds: PCDHGA5, CTXL, ..., HCMOGT-1 (total: 522) > geneIdType: Symbol > collectionType: Broad > bcCategory: c3 (Motif) > bcSubCategory: NA > details: use 'details(object)' >> details(C3coll[[1]]) > setName: RGAGGAARY_V$PU1_Q6 > geneIds: PCDHGA5, CTXL, ..., HCMOGT-1 (total: 522) > geneIdType: Symbol > collectionType: Broad > bcCategory: c3 (Motif) > bcSubCategory: NA > setIdentifier: c3:261 > description: Genes with promoter regions [-2kb,2kb] around transcription > start site containing the > motif RGAGGAARY which matches annotation for SPI1: spleen focus forming > virus (SFFV) proviral integ > ration oncogene spi1 > (longDescription available) > organism: Human,Mouse,Rat,Dog > pubMedIds: > urls: msigdb_v2.5.xml > contributor: Xiaohui Xie > setVersion: 0.0.1 > creationDate: Thu Jul 10 16:59:23 2008 > > invocation of the longDescription method against C3coll[[1]] leads > to an interesting structure that will need to be parsed -- seems to be > in a marked up medline format. > > once you have found the gene sets you are interested in, GSEABase > contains additional infrastructure to convert the identifiers for > genes used in MSIGDB to array probe set identifiers or entrez identifiers, > etc. > > >> >> Thanks. >> >> -- >> Paul Geeleher >> Department of Mathematics >> National University of Ireland >> Galway >> Ireland >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- Paul Geeleher School of Mathematics, Statistics and Applied Mathematics National University of Ireland Galway Ireland