Question: folate pathway is missing a key gene, MTHFR
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gravatar for Tomas Radivoyevitch
15.3 years ago by
Tomas Radivoyevitch70 wrote:
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)) 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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ADD COMMENTlink modified 15.3 years ago by John Zhang2.9k • written 15.3 years ago by Tomas Radivoyevitch70
Answer: folate pathway is missing a key gene, MTHFR
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gravatar for John Zhang
15.3 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
>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 > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENTlink written 15.3 years ago by John Zhang2.9k
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