Get Gene annotation (GO terms)
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David ▴ 860
@david-3335
Last seen 3.6 years ago
Hi, Which package should i use to convert a list of gene names (ACSL1,ADAMTSL1,ATG2B,BACH2...) into Go id. The idea behind is to get a list of significant GO terms based on the input genes).thanks for pointing me to right direction. thanks, david
GO convert GO convert • 1.8k views
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 5.2 years ago
United States
What species? Those look like human gene symbosl, so I will give an example for that: library(org.Hs.eg.db) sym <- c("ACSL1","ADAMTSL1","ATG2B","BACH2") ## Then you can just merge together the GO to entrez gene mappings with the SYMBOL to entrez gene mappings like this: merge(toTable(org.Hs.egSYMBOL2EG[sym]), toTable(org.Hs.egGO), by.x= "gene_id", by.y="gene_id") Does that make sense? Marc On 03/17/2011 02:11 PM, David martin wrote: > Hi, > Which package should i use to convert a list of gene names > (ACSL1,ADAMTSL1,ATG2B,BACH2...) into Go id. The idea behind is to get > a list of significant GO terms based on the input genes).thanks for > pointing me to right direction. > > thanks, > david > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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Perfect it's human, I guess i can then use any of the GO packages to get signficant Goterms. Which one would you suggest ? On 03/17/2011 10:16 PM, Marc Carlson wrote: > What species? Those look like human gene symbosl, so I will give an > example for that: > > library(org.Hs.eg.db) > sym <- c("ACSL1","ADAMTSL1","ATG2B","BACH2") > ## Then you can just merge together the GO to entrez gene mappings with > the SYMBOL to entrez gene mappings like this: > merge(toTable(org.Hs.egSYMBOL2EG[sym]), toTable(org.Hs.egGO), by.x= > "gene_id", by.y="gene_id") > > Does that make sense? > > > Marc > > > On 03/17/2011 02:11 PM, David martin wrote: >> Hi, >> Which package should i use to convert a list of gene names >> (ACSL1,ADAMTSL1,ATG2B,BACH2...) into Go id. The idea behind is to get >> a list of significant GO terms based on the input genes).thanks for >> pointing me to right direction. >> >> thanks, >> david >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Hi David, For human you want to use org.Hs.eg.db. Other packages may also contain GO terms but not mapped onto the correct set of genes. So if instead you had used org.Mm.eg.db, you would find GO terms mapped only onto mouse genes and symbols. Marc On 03/17/2011 02:21 PM, David martin wrote: > Perfect it's human, > I guess i can then use any of the GO packages to get signficant > Goterms. Which one would you suggest ? > > On 03/17/2011 10:16 PM, Marc Carlson wrote: >> What species? Those look like human gene symbosl, so I will give an >> example for that: >> >> library(org.Hs.eg.db) >> sym <- c("ACSL1","ADAMTSL1","ATG2B","BACH2") >> ## Then you can just merge together the GO to entrez gene mappings with >> the SYMBOL to entrez gene mappings like this: >> merge(toTable(org.Hs.egSYMBOL2EG[sym]), toTable(org.Hs.egGO), by.x= >> "gene_id", by.y="gene_id") >> >> Does that make sense? >> >> >> Marc >> >> >> On 03/17/2011 02:11 PM, David martin wrote: >>> Hi, >>> Which package should i use to convert a list of gene names >>> (ACSL1,ADAMTSL1,ATG2B,BACH2...) into Go id. The idea behind is to get >>> a list of significant GO terms based on the input genes).thanks for >>> pointing me to right direction. >>> >>> thanks, >>> david >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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Unless you meant that you are intending to do hypergeometric testing, (which is a different question). If that was your question, then GOstats works well, although there are indeed many to choose from. Marc On 03/17/2011 02:40 PM, Marc Carlson wrote: > Hi David, > > For human you want to use org.Hs.eg.db. > > Other packages may also contain GO terms but not mapped onto the > correct set of genes. So if instead you had used org.Mm.eg.db, you > would find GO terms mapped only onto mouse genes and symbols. > > > Marc > > > > On 03/17/2011 02:21 PM, David martin wrote: >> Perfect it's human, >> I guess i can then use any of the GO packages to get signficant >> Goterms. Which one would you suggest ? >> >> On 03/17/2011 10:16 PM, Marc Carlson wrote: >>> What species? Those look like human gene symbosl, so I will give an >>> example for that: >>> >>> library(org.Hs.eg.db) >>> sym <- c("ACSL1","ADAMTSL1","ATG2B","BACH2") >>> ## Then you can just merge together the GO to entrez gene mappings with >>> the SYMBOL to entrez gene mappings like this: >>> merge(toTable(org.Hs.egSYMBOL2EG[sym]), toTable(org.Hs.egGO), by.x= >>> "gene_id", by.y="gene_id") >>> >>> Does that make sense? >>> >>> >>> Marc >>> >>> >>> On 03/17/2011 02:11 PM, David martin wrote: >>>> Hi, >>>> Which package should i use to convert a list of gene names >>>> (ACSL1,ADAMTSL1,ATG2B,BACH2...) into Go id. The idea behind is to get >>>> a list of significant GO terms based on the input genes).thanks for >>>> pointing me to right direction. >>>> >>>> thanks, >>>> david >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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Yes that's correct. I will give Gostats a try !! thanks. On 03/17/2011 10:43 PM, Marc Carlson wrote: > Unless you meant that you are intending to do hypergeometric testing, > (which is a different question). If that was your question, then GOstats > works well, although there are indeed many to choose from. > > Marc > > > > On 03/17/2011 02:40 PM, Marc Carlson wrote: >> Hi David, >> >> For human you want to use org.Hs.eg.db. >> >> Other packages may also contain GO terms but not mapped onto the >> correct set of genes. So if instead you had used org.Mm.eg.db, you >> would find GO terms mapped only onto mouse genes and symbols. >> >> >> Marc >> >> >> >> On 03/17/2011 02:21 PM, David martin wrote: >>> Perfect it's human, >>> I guess i can then use any of the GO packages to get signficant >>> Goterms. Which one would you suggest ? >>> >>> On 03/17/2011 10:16 PM, Marc Carlson wrote: >>>> What species? Those look like human gene symbosl, so I will give an >>>> example for that: >>>> >>>> library(org.Hs.eg.db) >>>> sym <- c("ACSL1","ADAMTSL1","ATG2B","BACH2") >>>> ## Then you can just merge together the GO to entrez gene mappings with >>>> the SYMBOL to entrez gene mappings like this: >>>> merge(toTable(org.Hs.egSYMBOL2EG[sym]), toTable(org.Hs.egGO), by.x= >>>> "gene_id", by.y="gene_id") >>>> >>>> Does that make sense? >>>> >>>> >>>> Marc >>>> >>>> >>>> On 03/17/2011 02:11 PM, David martin wrote: >>>>> Hi, >>>>> Which package should i use to convert a list of gene names >>>>> (ACSL1,ADAMTSL1,ATG2B,BACH2...) into Go id. The idea behind is to get >>>>> a list of significant GO terms based on the input genes).thanks for >>>>> pointing me to right direction. >>>>> >>>>> thanks, >>>>> david >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor at r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: >>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
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