Drug Pathway Decipherer Version 1.0 22/11/2007 ======================= The Drug Pathway Decipher is implemented in java. This document is an instruction for how to use the system. File structure: expression (Folder): a collection of gene expression data to be evaluated against; pathway (Folder): a collection of pathways to be evaluated; result (Folder): the result of pathway analysis; Main.java: the main function of our system; GeneExpression.java: processing gene expression data; SigPathway.java: processing signaling pathways; GenPathway.java: processing genetic pathways. Instruction for use: Step1: put the pathways to be evaluated into the folder; Step2: put the gene expression to be evaluated against into the folder; Step3: create an empty folder; Step4: select threshold for p-value cutoff and/or FDR control (at least one); Step5: compile the source code: javac Main.java; Step6: run the system, for example, we set 0.05 for p-value and 0.5 for FDR control: java Main p=0.05,fdr=0.5; File Format: A gene expression file is in CVS format: ,,,[,...] A pathway file requires the keywords ``Interaction:'' and ``Association:'' as the symbols for protein-protein interaction and protein-gene association. Each token is seperated with a or . The regulation type can be either $stimulation or $suppression. An Example: Interaction: [ ] ... [ ] Association: [ ... ] ... Credits: The Drug Pathway Decipher was implemented by Difeng Dong.