PANTHER in R.... Gene lists in sigPathway?
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Voke AO • 760
@voke-ao-4830
Last seen 6.5 years ago
Hi all, Is there any way to execute PANTHER in R? And is there any possible way sigPathway works with gene lists in place of expression data? Thanks. -Avoks
sigPathway sigPathway • 1.4k views
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@felipe-riveroll-aguirre-5264
Last seen 6.5 years ago
There is no bioconductor project, for pantherdb, but you can get a tab separated file with entrezID and logFC data from limma for example, and upload the generated file to the pantherdb website and use Tools>GENE EXPRESSION DATA ANALYSIS>Analyze a list of genes with expression values to get a pathway analysis May be this could help you, I had done somethin similar with SPIA to get a KEGG heatmap from a selected pathway here: http://translate.google.com/translate?sl=auto&tl=en&js=n&prev=_t&hl=en &ie=UTF-8&layout=2&eotf=1&u=http://blog.feliperiveroll.name/obtencion- de-un-heatmap-para-una-via-de-senalizacion/&act=url The main idea was to parse the SPIA pathway output link, and get the KEGG identifier for this pathway, the KEGG identifier of an object in this pathway, and finally the logFC value, and feed a external python script to get the heatmap. You can read more about the SPIA (and pathway) analysis, here http://gettinggeneticsdone.blogspot.mx/2012/03/pathway-analysis-for- high-throughput.html And also, panther could help you for a gene analysis for entrezID's Hope it helps Felipe Antonio Riveroll Aguirre, QFB Departamento de Bioqu?mica Laboratorio 26 CINVESTAV, M?xico D. F. CP 07360 Tel. +52 (55)?5747-3800 ext 5217 Celular. +52 (55) 3351-2251 Sitio web: http://www.feliperiveroll.name 2012/5/21 Ovokeraye Achinike-Oduaran <ovokeraye at="" gmail.com="">: > Hi all, > > Is there any way to execute PANTHER in R? And is there any possible > way sigPathway works with gene lists in place of expression data? > > Thanks. > > -Avoks > > _______________________________________________ > 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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Voke AO • 760
@voke-ao-4830
Last seen 6.5 years ago
Hi Felipe, Thanks. The thing is that I have genes from both GWAS and DE analysis from Limma in one list. So they don't all have logFC values, hence my question about gene lists and not necessarily gene sets. I ran my list through the PANTHER web interface and got some results but I just wanted to know if it had an R implementation. DAVIDQuery() might work if it gives the same options as is web interface of choosing the PANTHER pathway option but I didn't find the instruction manual very straightforward. Thanks again. -Avoks On 22 May 2012, at 6:17 AM, Felipe Riveroll Aguirre <friveroll at="" gmail.com=""> wrote: > Sorry I forget to write, this text for the first paragraph > > There is no bioconductor project, for pantherdb, but you can get a tab > separated file with entrezID and logFC data from limma for example, > and upload the generated file to the pantherdb website Tools>GENE > EXPRESSION DATA ANALYSIS>Analyze a list of genes with expression > values > > > Felipe Antonio Riveroll Aguirre > Salaverry 244. Interior 3 > Col. Residencial Zacatenco > Del. Gustavo A. Madero > CP 07360 > Ciudad de M?xico, M?xico > Celular: (55)3351-2251 > > > 2012/5/21 Felipe Riveroll Aguirre <friveroll at="" gmail.com="">: >> For the first question. >> >> There is no bioconductor project, for pantherdb, but you can get a tab >> separated file with entrezID and logFC data from limma for example
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May be you can get the limma logFC associated values, for associated GWAS genes, in the example from SPIA, I started only with entrezID's from KEGG link, and grab the logFC values from limma in sig_genes vector sig_genes <- subset(top, adj.P.Val<0.01)$logFC names(sig_genes) <- subset(top, adj.P.Val<0.01)$ENTREZ with this code genes.both <- sig_genes[which(names(sig_genes) %in% genes.via.sel)] Where genes.via.sel, was a gene list set of entrezID's to get limma associated values. So you can do an approach like this to get associated logFC values from associated GWAS genes Also there is another server I known for gene lists http://www.bioprofiling.de/R_spider.html Here you get an analysis combining signaling and metabolic pathways from Reactome and KEGG databases. So, R only helps to get the required inputs, for external web appz, or you can download pantherdb database and write an script for automate the whole process, from R output Best, Felipe 2012/5/22 Ovokeraye Achinike-Oduaran <ovokeraye at="" gmail.com="">: > > Hi Felipe, > > Thanks. The thing is that I have genes from both GWAS and DE analysis from Limma in one list. So they don't all have logFC values, hence my question about gene lists and not necessarily gene sets. I ran my list through the PANTHER web interface and got some results but I just wanted to know if it had an R implementation. > > DAVIDQuery() might work if it gives the same options as is web interface of choosing the PANTHER pathway option but I didn't find the instruction manual very straightforward. > > Thanks again. > > -Avoks >
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Thanks a bunch, Felipe. Regards, Avoks On Tue, May 22, 2012 at 6:45 PM, Felipe Riveroll Aguirre <friveroll at="" gmail.com=""> wrote: > May be you can get the limma logFC associated values, for associated > GWAS genes, in the example from SPIA, I started only with entrezID's > from KEGG link, and grab the logFC values from limma in sig_genes > vector > > sig_genes <- subset(top, adj.P.Val<0.01)$logFC > names(sig_genes) <- subset(top, adj.P.Val<0.01)$ENTREZ > > with this code > > genes.both <- sig_genes[which(names(sig_genes) %in% genes.via.sel)] > > Where ?genes.via.sel, was a gene list set of entrezID's to get limma > associated values. > > So you can do an approach like this to get associated logFC values > from associated GWAS genes > > Also there is another server I known for gene lists > > http://www.bioprofiling.de/R_spider.html > > Here you get an analysis combining signaling and metabolic pathways > from Reactome and KEGG databases. > > So, R only helps to get the required inputs, for external web appz, or > you can download pantherdb database and write an script for automate > the whole process, from R output > > Best, > > Felipe > > 2012/5/22 Ovokeraye Achinike-Oduaran <ovokeraye at="" gmail.com="">: >> >> Hi Felipe, >> >> Thanks. The thing is that I have genes from both GWAS and DE analysis from Limma in one list. So they don't all have logFC values, hence my question about gene lists and not necessarily gene sets. I ran my list through the PANTHER web interface and got some results but I just wanted to know if it had an R implementation. >> >> DAVIDQuery() might work if it gives the same options as is web interface of choosing the PANTHER pathway option but I didn't find the instruction manual very straightforward. >> >> Thanks again. >> >> -Avoks >> > > _______________________________________________ > 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