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Question: Pathview with minor species
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gravatar for Luo Weijun
4.8 years ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
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/Bacter ia.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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