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

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