[BioC] Pathview with minor species

Luo Weijun luo_weijun at yahoo.com
Wed Jan 29 21:25:56 CET 2014

Someone asked a similar question on using pathview or gage with honey bee. Here is the solution:

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:
Column 2-6 should be (Entrez) GeneID, Symbol, LocusTag, Synonyms, dbXrefs. Then follow the route described in the honey bee case.


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).
 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,

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