I am trying to get a KEGG pathway heat map with this python script https://github.com/ajmazurie/color-KEGG- pathways/blob/master/README.rst Till now I get this script but KEGG does find entrez id in the pathway from my list. #Get a list from genes in KEGG pathway in the expressionSet eset.LWT probeids <- get("04010", mouse4302PATH2PROBE) names.MAPK <- intersect(probeids,featureNames(eset.LWT)) #Select only the genes differentially expressed by limma contrast matrix names.MAPK.selected_WT <- intersect(liver_WT.list$ID, names.MAPK) #Get a table with fold change values from selected genes in the KEGG pathway MAPK <- liver_WT.list[ which(names.MAPK.selected_E %in% liver_E.list$ID),1:2] #Add Entrez ID MAPK$ENTREZ<-unlist(as.list(mouse4302ENTREZID[MAPK$ID])) MAPK<-MAPK[!is.na(MAPK$ENTREZ),] MAPK<-MAPK[!duplicated(MAPK$ENTREZ),] write.table(MAPK, "MAPK_WT.txt", sep="\t", quote=FALSE) Could you help me to get an input for color-KEGG-pathways? R version 2.15.0 (2012-03-30) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=Spanish_Mexico.1252 LC_CTYPE=Spanish_Mexico.1252 [3] LC_MONETARY=Spanish_Mexico.1252 LC_NUMERIC=C [5] LC_TIME=Spanish_Mexico.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mouse4302.db_2.7.1 org.Mm.eg.db_2.7.1 RSQLite_0.11.1 [4] DBI_0.2-5 AnnotationDbi_1.18.0 limma_3.12.0 [7] affy_1.34.0 Biobase_2.16.0 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] affyio_1.24.0 BiocInstaller_1.4.4 IRanges_1.14.2 [4] preprocessCore_1.18.0 stats4_2.15.0 tools_2.15.0 [7] zlibbioc_1.2.0 [[alternative HTML version deleted]]

Hi. Finally I found how to get an input file, for color-KEGG-pathways script. After following this tutorial http://gettinggeneticsdone.blogspot.mx/2012/03/pathway-analysis-for- high-throughput.html you get a list of pathways with highlighted genes, then if you wanna get a heat map, from SPIA maped genes, you could use this pyhon script https://github.com/ajmazurie/color-KEGG-pathways/, but you need an input with these values, for every gene KEGG_Pathway_ID,KEGG_obj_ID,value This is my code, but I dont known how to get the list of the SPIA pathway linked genes, I do this step manually deleting the web address and replacing "+" with ", " in a text editor, from the KEGGLINK. Could you help me to get this with R? #Genes linked with SPIA result from 1st pathway hsa04510 <- c(3678, 3680, 2316, 10398, 2534, 1278, 1282, 1293, 5649, 7058, 7148, 7450, 857, 858, 3479, 5155, 7424, 3725) #Get a subset of logFC values for pathway linked genes hsa04510.exp <- sig_genes[which(names(sig_genes) %in% hsa04510)] #Load the results as data frame hsa04510.df <- as.data.frame(hsa04510.exp) #Get the first col for the output needed for the python script color-KEGG-pathways # https://github.com/ajmazurie/color-KEGG- pathways/blob/master/README.rst ruta <- rep("hsa04510", length(hsa04510)) #Get the second Col hsa04510.genes.out <- c(paste("hsa:",names(hsa04510.exp), sep="")) #Now get the data frame with the required output hsa04510.color.input <- data.frame (ruta, hsa04510.genes.out, hsa04510.df[[1]]) #Write to a file write.table(hsa04510.color.input, "hsa04510.color.input.csv", sep=",", quote=FALSE, row.names = FALSE, col.names = FALSE) 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 2012/5/3 Felipe Riveroll Aguirre <friveroll at="" gmail.com=""> > > I am trying to get a KEGG pathway heat map with this python script > https://github.com/ajmazurie/color-KEGG- pathways/blob/master/README.rst >