help for pathways
1
0
Entering edit mode
@alberto-goldoni-711
Last seen 10.2 years ago
Hi to everybody, i have a list of genes and i would like to obtain for all genes the pathway in witch it is involved. there are one script or one package just for it? -- ----------------------------------------------------- Dr Alberto Goldoni, PhD Medical Genetics Unit S. Orsola-Malpighi Hospital Via Massarenti n.9, Pad 11 40100 Bologna, Italy Mobile Phone: 338-4145970 Fax: 051-636-4004 alberto.goldoni at eurogene.org www.eurogene.org www.lagem.it
Genetics Genetics • 909 views
ADD COMMENT
0
Entering edit mode
SAURIN ★ 1.1k
@saurin-799
Last seen 10.2 years ago
hi, It will give you heatmap so, you will see which genes are involved in those pathways and how their expression intensity look like. About Pathway to HEATMAP # Variable explanation: # esetSub2 = expression matirx # chiptype = annotation found from GeneChip, here 'hgu95a' # envPath2Probes = Environment # envGeneNames <- hgu95aGENENAME; # envPath2Probes <- hgu95aPATH2PROBE; # Generate Pathway Heatmap   All_DE_Pathway <- aafPathway(geneNames(esetSub2), chiptype);   unique(sapply(All_DE_Pathway, length));   pathlist <- do.call("c", All_DE_Pathway);   pathL <- length(pathlist);   pathmatrix <- sapply(pathlist, attributes);   pathnamesX <- unique(t(pathmatrix));   kegg <- as.list(envPath2Probes);   pathRow <-  as.numeric(nrow(pathnamesX));   if(pathL >=1)   {     for(i in 1:pathRow)     {       pathID <- pathnamesX[,"id"][i];       pathID <- as.character(unlist(pathID));       pathName <- as.character(unlist(pathnamesX[,"name"][i]));       pathName <- trimWhiteSpace(pathName);       pathName <- sub("/", "_", pathName);       pathName <- sub(" ", "_", pathName);       pathName <- sub("  ", "_", pathName);       pathName <- sub("   ", "_", pathName);       pathName <- sub(" ", "_", pathName);       pathName <- sub("-", "_", pathName);       pathFile <- paste("Pathway",pathName,".jpeg",sep = "_");       pathSub <- paste(pathName,"Legend: Red = High, Blue = Low, White = Medium",sep = "  ");       pathSub <- paste("Date of Analysis:",date(),pathSub,sep = "  ");       Pathway2Heatmap(pathID,pathFile,pathSub); # check out the function below     }   } # if ends here # ########################################################### Pathway2Heatmap <- function(pathway,file,Hsub) {   kegg <- as.list(envPath2Probes);   pathProbes <- as.matrix(kegg[[pathway]]); # genes extracted from pathway   esetSub2Genes <- as.matrix(geneNames(esetSub2));   temp <- as.matrix(rbind(unique(esetSub2Genes),unique(pathProbes)));   temp1 <- as.matrix(temp[ as.matrix(duplicated(temp,))]);   exp2 <- esetSub2[temp1];   exp2X <-  exprs(exp2);   pathDEGenes <- as.matrix(geneNames(exp2));   pathDEGeneNames <- mget(unique(pathDEGenes),env = envGeneNames,ifnotfound="No Annotation For this Probe");   row.names(exp2X) <- pathDEGeneNames;   colnames(exp2X) <- samples;   if (nrow(exp2X) > 1)   {     jpeg(filename= file,width=2000,height=2000);     row.dist <- as.dist(1 - cor(t(exp2X)));     Hsub <- c("Generated by EXAMPLE");     gmpalette <- bluered(64); heatmap.2(exp2X,col=gmpalette,Colv= FALSE,Rowv = as.dendrogram(hclust(row.dist,method="centroid")),scale="row",key=TRUE ,keysize=0.60,symkey=FALSE,density.info="none",trace="none",margins=c( 5,85),cexRow=1,cexCol=1, sub=Hsub,cex.sub=1); dev.off(which = dev.cur());     print("Pathway Heat map done");   }#if }#pathway2heatmap ########################################################### For more info. to run free web based analysis on your data http://proteogenomics.musc.edu/ma/arrayQuest.php?page=home&act=manage& process=Methods_Library_List Saurin --- On Tue, 7/29/08, Alberto Goldoni <alberto.goldoni@eurogene.org> wrote: From: Alberto Goldoni <alberto.goldoni@eurogene.org> Subject: [BioC] help for pathways To: bioconductor-bounces@stat.math.ethz.ch, "Bioconductor" <bioconductor@stat.math.ethz.ch> Date: Tuesday, July 29, 2008, 11:08 AM Hi to everybody, i have a list of genes and i would like to obtain for all genes the pathway in witch it is involved. there are one script or one package just for it? -- ----------------------------------------------------- Dr Alberto Goldoni, PhD Medical Genetics Unit S. Orsola-Malpighi Hospital Via Massarenti n.9, Pad 11 40100 Bologna, Italy Mobile Phone: 338-4145970 Fax: 051-636-4004 alberto.goldoni@eurogene.org www.eurogene.org www.lagem.it _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
ADD COMMENT

Login before adding your answer.

Traffic: 958 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6