How to cluster genes based on their GO term in Arabidopsis?
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Xiaohui Wu ▴ 280
@xiaohui-wu-4141
Last seen 6.6 years ago
Hi all, I want to cluster some genes based on their GO term annotation information in Arabidopsis and plot the profile. I tried some packages in Bioconductor including 'goProfiles', 'org.Hs.eg.db', but it says "No ancestors found for this GOTermsList ". The code I tested is as follows: ---------------------- require(goProfiles) require(org.At.tair.db) #first, transform tair ID to entrez ID x <- org.At.tairENTREZID mapped_genes <- mappedkeys(x) tairENID <- as.list(x[mapped_genes]) #then, plot the profile arab.MF <- basicProfile(genelist=tairENID, onto = "MF", level = 2, orgPackage = "org.At.tair.db") --------------------- For the example of 'basicProfile' in goProfiles, it works, but it is for human, the code is: ---------------------- require(goProfiles) data(prostateIds) welsh.MF <- basicProfile(welsh01EntrezIDs, onto = "MF", level = 2, orgPackage = "org.Hs.eg.db") singh.MF <- basicProfile(singh01EntrezIDs, onto = "MF",level = 2, orgPackage = "org.Hs.eg.db") welsh.singh.MF <- mergeProfilesLists(welsh.MF,singh.MF, profNames = c("Welsh", "Singh")) printProfiles(welsh.singh.MF, percentage = TRUE) plotProfiles(welsh.MF, aTitle = "Welsh (2001). Prostate cancer data") ---------------------- Can you see what the problem is? Or is there any other way to cluster the genes and plot the profile? Thanking you, Rae [[alternative HTML version deleted]]
GO Cancer Prostate goProfiles GO Cancer Prostate goProfiles • 691 views
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@james-w-macdonald-5106
Last seen 7 hours ago
United States
Hi Rae, Xiaohui Wu wrote: > Hi all, > > I want to cluster some genes based on their GO term annotation information in Arabidopsis and plot the profile. I tried some packages in Bioconductor including 'goProfiles', 'org.Hs.eg.db', but it says "No ancestors found for this GOTermsList ". > > The code I tested is as follows: > ---------------------- > require(goProfiles) > require(org.At.tair.db) > > #first, transform tair ID to entrez ID > x <- org.At.tairENTREZID > mapped_genes <- mappedkeys(x) > tairENID <- as.list(x[mapped_genes]) > > #then, plot the profile > arab.MF <- basicProfile(genelist=tairENID, onto = "MF", level = 2, orgPackage = "org.At.tair.db") > --------------------- > > For the example of 'basicProfile' in goProfiles, it works, but it is for human, the code is: > ---------------------- > require(goProfiles) > data(prostateIds) > welsh.MF <- basicProfile(welsh01EntrezIDs, onto = "MF", level = 2, orgPackage = "org.Hs.eg.db") > singh.MF <- basicProfile(singh01EntrezIDs, onto = "MF",level = 2, orgPackage = "org.Hs.eg.db") > welsh.singh.MF <- mergeProfilesLists(welsh.MF,singh.MF, profNames = c("Welsh", "Singh")) > printProfiles(welsh.singh.MF, percentage = TRUE) > plotProfiles(welsh.MF, aTitle = "Welsh (2001). Prostate cancer data") > ---------------------- > > Can you see what the problem is? Or is there any other way to cluster the genes and plot the profile? Yes. The help page for this function is in error. The argument 'genelist' isn't actually supposed to be a list, even though you might surmise that from the argument name, and be confirmed by the argument description: genelist: List of genes on which the Profile has to be based If you look at the example you show above > class(singh01EntrezIDs) [1] "character" and the example for basicProfile > class(CD4LLids) [1] "character" > head(CD4LLids) [1] "10160" "10461" "10579" "10611" "10629" "10786" You can see that the input is actually supposed to be a character vector. Or maybe a list of character vectors (not really sure, and don't have the time or inclination to dig deeper), but certainly not a list of character vectors of length one. If I replace tairENID with mapped.genes from your code above, I get > print(arab.MF) $MF Description GOID Frequency 7 antioxidant activity GO:0016209 132 4 binding GO:0005488 10036 1 catalytic activity GO:0003824 7767 8 channel regulator activity GO:0016247 0 13 chemoattractant activity GO:0042056 0 15 chemorepellent activity GO:0045499 0 5 electron carrier activity GO:0009055 484 10 enzyme regulator activity GO:0030234 332 9 metallochaperone activity GO:0016530 4 17 molecular transducer activity GO:0060089 374 16 nutrient reservoir activity GO:0045735 58 6 proteasome regulator activity GO:0010860 0 12 protein tag GO:0031386 4 2 structural molecule activity GO:0005198 499 11 transcription regulator activity GO:0030528 1886 14 translation regulator activity GO:0045182 5 3 transporter activity GO:0005215 1216 Best, Jim > > Thanking you, > > Rae > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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