[BioC] folate pathway is missing a key gene, MTHFR

[John Zhang]

>Hi All,
>FYI, I noticed that MTHFR, a key gene of the folate pathway, is not in the
>pathway
>00670 "One carbon pool by folate,"  though it certainly should be. For
>example, this code
>
>library(Biobase)
>library(hgu133a)
>library(KEGG)
>IDs=get("00670", env = hgu133aPATH2PROBE);IDs
>as.character(multiget(IDs, env = hgu133aSYMBOL))
>

You were probably using the developmental version of the annotation packages 
(1.6.1) where (I found yesterday) the PATH2PROBE environment is broken. I will 
do another build next week to fix the problem. I tried your code against the 
release version (1.5.1). The results seem to be right.

> library(hgu133a)
> library(KEGG)
> IDs=get("00670", env = hgu133aPATH2PROBE);IDs
 [1] "217104_at"   "210242_x_at" "203433_at"   "201761_at"   "215798_at"  
 [6] "205208_at"   "220604_x_at" "202533_s_at" "48808_at"    "202532_s_at"
[11] "202534_x_at" "212378_at"   "216990_at"   "210005_at"   "212379_at"  
[16] "217445_s_at" "204294_at"   "202309_at"   "217070_at"   "206800_at"  
[21] "217071_s_at" "203774_at"   "208758_at"   "209980_s_at" "214437_s_at"
[26] "202589_at"   "213645_at"   "217684_at"   "217690_at"  
> as.character(multiget(IDs, env = hgu133aSYMBOL))
 [1] "MTHFS"  "MTHFS"  "MTHFS"  "MTHFD2" "FTHFD"  "FTHFD"  "FTCD"   "DHFR"  
 [9] "DHFR"   "DHFR"   "DHFR"   "GART"   "GART"   "GART"   "GART"   "GART"  
[17] "AMT"    "MTHFD1" "MTHFR"  "MTHFR"  "MTHFR"  "MTR"    "ATIC"   "SHMT1" 
[25] "SHMT2"  "TYMS"   "TYMS"   "TYMS"   "TYMS"



>fails to pick up these three probe sets for MTHFR:
>
>206800_at MTHFR 1p36.3  5,10-methylenetetrahydrofolate reductase (NADPH)
>217070_at MTHFR 1p36.3  5,10-methylenetetrahydrofolate reductase (NADPH)
>217071_s_at MTHFR 1p36.3  5,10-methylenetetrahydrofolate reductase (NADPH)
>
>Tom
>
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Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084