[BioC] R pathview and mouse

[Luo Weijun]

Scott,
Gene symbols and other IDs are case sensitive. For mouse and rat, most OFFICIAL gene symbols are initial upper case only, while all upper cases for human and many other species. For example, some mappable gene symbols (from your list) for mouse would be like Cd74, Mgp and Cd52, while they should be CD74, MGP and CD52 for human.
You may tried gene symbol search at NCBI like http://www.ncbi.nlm.nih.gov/gene/?term=CD52 and look at the results for different species. 
Weijun


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On Thu, 1/9/14, Scott wrote:

 Subject: R pathview and mouse

 Date: Thursday, January 9, 2014, 4:41 PM

 Hello Weijun,

 I am trying to map mouse gene names to entrez ids using the
 id2eg in your path view tool.  Below shows what I
 did.  The variable “T” holds the data, and I do a
 map, but none of the genes get mapped to entrez gene
 ids.  However, if I use human (“Hs”) then it
 works.  Do you know what is wrong?


 > biocLite("org.Mm.eg.db")

 > T
       H2-AB1   
    HSP105     
    CD74     
    GP38         
 MGP         CD52 
    TMEM176B       
 IFI27       LAPTM5   
     TGFBI     HSP90AB1 
     3.880227 
    3.429302 
    3.417246 
    3.164127 
    2.932691 
    2.852793 
    2.665297 
    2.564207 
    2.534474 
    2.366048     2.301527


 > T.id.map <- id2eg(ids = names(T), category =
 gene.idtype.list[1], org = "Mm")

 > T.id.map
       SYMBOL     
    EntrezGene
  [1,] "H2-AB1"       "" 
       
  [2,] "HSP105"       "" 
       
  [3,] "CD74"         "" 
       
  [4,] "GP38"         "" 
       
  [5,] "MGP"          "" 
       
  [6,] "CD52"         "" 
       
  [7,] "TMEM176B"     ""   
     
  [8,] "IFI27"        ""   
     
  [9,] "LAPTM5"       "" 
       
 [10,] "TGFBI"        ""   
     
 [11,] "HSP90AB1"     ""   
     


 However, if I use human then it works.


 > T.id.map <- id2eg(ids = names(T), category =
 gene.idtype.list[1], org = "Hs")
 > T.id.map
       SYMBOL     
    EntrezGene
  [1,] "H2-AB1"       "" 
       
  [2,] "HSP105"       "" 
       
  [3,] "CD74"     
    "972"     
  [4,] "GP38"         "" 
       
  [5,] "MGP"          "4256" 
   
  [6,] "CD52"     
    "1043"    
  [7,] "TMEM176B" 
    "28959"   
  [8,] "IFI27"        "3429"   

  [9,] "LAPTM5"       "7805" 
   
 [10,] "TGFBI"        "7045"   

 [11,] "HSP90AB1"     "3326"   



 thanks
 Scott