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Question: Pathview with minor species
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gravatar for Luo Weijun
4.6 years ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
I forgot to mention that in pathview vignette there is a dedicated section covering on species related issues, i.e. Section 7.5 ?Working with species?: http://bioconductor.org/packages/release/bioc/vignettes/pathview/inst/ doc/pathview.pdf I just noticed that locus tag is used as the default gene ID for KEGG pathways for B. subtilis (bsu). This is actually true for many bacteria and other minor species (including E coli K12). KEGG does not specify the default gene ID type explicitly, but you may find this out for your species in korg data (the kegg.geneid column). > data(korg) > ri=which(korg[,1]=="bsu") > korg[ri,] kegg.code scientific.name common.name entrez.gnodes "bsu" "Bacillus subtilis" "" "0" kegg.geneid ncbi.geneid "BSU00020" "939970" So you can actually do it in a simple way. You don?t have to map your gene IDs, just specify gene.idtype="kegg" when calling pathview. My analysis with simulated bsu data works well. bsu.dat.kegg <- sim.mol.data(mol.type="gene",id.type="kegg",species="bsu",nmol=3000) head(bsu.dat.kegg) BSU13160 BSU11080 BSU23500 BSU02510 BSU19920 BSU20590 -1.15259948 0.46416071 0.72893247 0.41061745 -1.46114720 -0.01890809 pv.out <- pathview(gene.data = bsu.dat.kegg, gene.idtype="kegg", pathway.id = "00010", species = "bsu", out.suffix = "bsu.kegg") A similar example was given on E coli K12 in page 20 of the vignette. I would suggest to go over section 7.5 ?Working with species? if you need to work on minor species. -------------------------------------------- Subject: Re: Pathview with minor species To: bioconductor at r-project.org Date: Wednesday, January 29, 2014, 3:25 PM Someone asked a similar question on using pathview or gage with honey bee. Here is the solution: http://seqanswers.com/forums/showthread.php?t=35472#6 Like honey bee, B. subtilis (bsu) is not a major species with Bioconductor gene annotation package as those listed in data(bods) under pathview package. similarly you need to map Locus_tags to Entrez gene ID manually. Again, you can download the gene_info data file (for all bacteria) from NCBI ftp site: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Archaea_Bacteria/Bacte ria.gene_info.gz Column 2-6 should be (Entrez) GeneID, Symbol, LocusTag, Synonyms, dbXrefs. Then follow the route described in the honey bee case. HTHs. -------------------------------------------- On Wed, 1/29/14, David wrote: Subject: Pathview with minor species Date: Wednesday, January 29, 2014, 11:09 AM Dear Mr Luo, In our course we got B. subtilis (bsu) microarray data and I want to visualize some expression changes with Pathview. But I have a problem. We got Locus_tags like BSU00010 and no gene IDs and I don't know whether Pathview can use it or not. I really don't understand the part about it in the vignette. So I thought of converting them to UniProt IDs. But first I wanted to do a test run. So I searched for the UniProt IDs of 3 genes of the glycolysis from B. subtilis and put them into a data.frame with fictional data (dummy). library(pathview) dummy<-data.frame(name=c("P18159","P80860","P13243"),ratio=c(1,0,-1) ,row.names="name") dummy<-as.matrix(dummy) pv.out <- pathview(gene.data = dummy[, "ratio"], pathway.id = "00010",species = "bsu", out.suffix = "dummy", kegg.native=T, gene.idtype="UNIPROT") When I tried it this way, an error occured: No proper gene [[elided Yahoo spam]] Afterwards I tested it with 3 genes from human and hsa as species and than it worked fine. Nothing I tried to solve the problem, worked. I have the latest version of Bioconductor and Pathview installed. Does Pathview not work with Bacillus subtilis subsp. subtilis 168 (=bsu) even though it's a KEGG organism? Or what am I doing wrong? I look forward to hearing from you. Sincerely yours, David
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