From owner-comp-bio@hgmp.mrc.ac.uk Tue Jan 9 21:54:55 2001 Return-Path: Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 110) id 09C9217B67; Tue, 9 Jan 2001 21:54:52 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6023) id 85B6617ADC; Tue, 9 Jan 2001 21:54:48 +0000 (GMT) Received: by mercury.hgmp.mrc.ac.uk (Postfix, from userid 6024) id 102F217ACE; Tue, 9 Jan 2001 11:47:21 +0000 (GMT) Received: from ashd1-1.relay.mail.uu.net (ashd1-1.relay.mail.uu.net [199.171.54.245]) by mercury.hgmp.mrc.ac.uk (Postfix) with ESMTP id 1E2144167D for ; Tue, 9 Jan 2001 11:47:05 +0000 (GMT) Received: from chiark.greenend.org.uk by mr0.ash.ops.us.uu.net with ESMTP (peer crosschecked as: chiark.greenend.org.uk [195.224.76.132]) id QQjxfj24566 for ; Tue, 9 Jan 2001 11:47:03 GMT Received: from news by chiark.greenend.org.uk with local (Exim 3.12 #2) id 14FxEz-0007pO-00 (Debian); Tue, 09 Jan 2001 11:47:01 +0000 To: bionet-biology-computational@uunet.uu.net From: Tim Cutts Newsgroups: bionet.biology.computational Subject: Re: Pathways and graphs Organization: Linux Unlimited Message-ID: References: <93aenb$udb$1@nnrp1.deja.com> X-Newsreader: trn 4.0-test70 (17 January 1999) Date: Tue, 9 Jan 2001 21:54:48 +0000 (GMT) Sender: owner-comp-bio@hgmp.mrc.ac.uk Precedence: bulk In article <93aenb$udb$1@nnrp1.deja.com>, wrote: >Hi, > > I am trying to relate pathway database and gene expression data. For >complete automation, one needs the pathways not in GIF image format(as >in kegg database) but in some text format that specifies the graph of >reaction labelled by enzymes or genes. Is anyone aware of text >representations of the pathways? Any help will >be great. Thanks a lot. You might want to investigate graphviz: http://www.research.att.com/sw/tools/graphviz/ I have found this to be a simple and useful textual representation of directed graphs. Tim. .