June 2007 - beg-sysbiol@psb.ugent.be

[Beg-sysbiol] code update
by Tom Michoel 29 Jun '07

29 Jun '07

I added my most recent LeMoNe code to the repository. Tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] [Fwd: meeting]
by Steven Maere 26 Jun '07

26 Jun '07

Would be good if we would be able to show something on Arabidopsis data... S -- ================================================================== Steven Maere, PhD Dept. of Plant Systems Biology Bioinformatics & Evolutionary Genomics research group VIB / Ghent University Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3810 fax: +32 9 331 3809 email: stmae(a)psb.UGent.be http://www.psb.UGent.be http://bioinformatics.psb.ugent.be/ ==================================================================

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[Beg-sysbiol] Dear All, could you (Postdocs) please have a look at this and give me some feedback within the next 2 weeks or so ...
by Yves Van de Peer 23 Jun '07

23 Jun '07

This could be good money (for some of you?) or new people ... Thanks in advance, Yves -------- Original Message -------- Subject: FP7--Things to do Date: Fri, 22 Jun 2007 14:46:36 +0300 From: Avi Levy <avi.levy(a)weizmann.ac.il> To: Avi Levy <avi.levy(a)weizmann.ac.il>, Naama Barkai <Barkai(a)wisemail.weizmann.ac.il>, Dani Zamir <zamir(a)agri.huji.ac.il>, Lothar Willmitzer <Willmitzer(a)mpimp-golm.mpg.de>, Thomas Altmann <Altmann(a)mpimp-golm.mpg.de>, FEUILLET Catherine <catherine.feuillet(a)clermont.inra.fr>, Boulos Chalhoub <chalhoub(a)evry.inra.fr>, "Mittelsten Scheid, Ortrun" <ortrun.mittelsten_scheid(a)gmi.oeaw.ac.at>, "ian bancroft (JIC)" <ian.bancroft(a)bbsrc.ac.uk>, Alan Schulman <alan.schulman(a)helsinki.fi>, Elisabetta Frascaroli <elisabetta.frascaroli(a)unibo.it>, Maarten Koornneef <koornnee(a)mpiz-koeln.mpg.de>, Michele Morgante <michele.morgante(a)uniud.it>, Wyatt Paul <wyatt.paul(a)biogemma.com>, Mark Aarts <mark.aarts(a)wur.nl>, Joost Keurentjes <Joost.keurentjes(a)wur.nl>, Anna Nadolska-Orczyk <a.orczyk(a)ihar.edu.pl>, Yves Van de Peer <yves.vandepeer(a)psb.ugent.be> Dear Heterosys participants, The participant list is close to complete. We need I think one or two more SMEs-- Suggestions are welcome. I attach a first document, describing in general terms the concept of the project. It is the fruit of discussions with Dani and Naama. I tried to write it as the best compromise I could between the wording of the call and reality. The general idea is to carry a comparative analysis of heterosis and ploidy responses in model species and crops and to try to link those responses to growth vigor phenotypes. Applications of large collaborative projects in FP7 are in two stages. The first stage has a deadline on Sept 11th. If it is approved we will be invited to submit a full proposal in Feb 2008. Funding (let's remain optimistic) should start by the end of 2008. Stage 1, is a ~20 pages application, it will be judged on 2 main criteria: Science and impact. What I need at this stage is explained in the attached document. As we did not meet yet as a group, the writing might take few drafts. With the summer vacations in the middle this means we should all do the effort to respond relatively quickly. Please send me the requested material within 10 days (July 2nd). All the best. Avi ============================================================= Avraham A. Levy Plant Sciences Department The Weizmann Institute of Sciences Rehovot, 76100 Israel Tel (W) 972 8 934 2734 Fax 972 8 934 4181 E-mail: avi.levy(a)weizmann.ac.il http://www.weizmann.ac.il/Plant_Sciences/levy/ ============================================================= -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://www.psb.ugent.be/bioinformatics/

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[Beg-sysbiol] Arabidopsis run results
by Eric Bonnet 23 Jun '07

23 Jun '07

/group/biocomp/projects/segal/java/ath_run0.tar The tar file contains: property file used to run the program log file results file (ath_run0.xml.gz) Results file is fairly big, so you need to allocate ~3 Gb to load it (java option: -Xmx3000m). Eric

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[Beg-sysbiol] [Fwd: RE: Thanks for the acceptance of my visit on July 20(Fri)-- Toru YAO/RIKEN]
by Yves Van de Peer 22 Jun '07

22 Jun '07

-------- Original Message -------- Subject: RE: Thanks for the acceptance of my visit on July 20(Fri)-- Toru YAO/RIKEN Date: Fri, 22 Jun 2007 07:21:12 +0200 From: Martin Kuiper <makui(a)psb.UGent.be> To: yao <yao(a)riken.jp> CC: Dirk Inze <dirk.inze(a)psb.UGent.be>, Yves Van de Peer <yves.vandepeer(a)psb.ugent.be>, Hilde Diegenant <hidie(a)psb.UGent.be> References: <02AE15DCD9DADE47925138968C2B9D371F2586(a)hermes.psb.UGent.be> <20070601082057.95A7.YAO(a)riken.jp> <20070614085953.8949.YAO(a)riken.jp> Dear Prof. Yao, You proposal is fine, I will be happy to host you. I propose that we organise two presentations for that morning (Kuiper, Van de Peer), and a tour through the laboratory. You should already know that there are not too many people working that day, as it is the period of the 'Ghent Festival', a local holiday. Many of us, however, still work. Kind regards, Martin Kuiper -----Original Message----- From: yao [mailto:yao@riken.jp] Sent: donderdag 14 juni 2007 1:20 To: yao Cc: Dirk Inze; Martin Kuiper; Yves Van de Peer; Hilde Diegenant Subject: Re: Thanks for the acceptance of my visit on July 20(Fri)-- Toru YAO/RIKEN Dear Prof.Dirk Inze and Prof.Martin Kuiper; I would like to confirm the time span to visit both of you on July 20 (Fri). I will be free whole day of July 20 by staying at a hotel in Brussell from 18 to 21. I think I will be able to arrive at Ghent around 9:30am of Friday. I don't want to disurbe so much your valuable time, so how about the time span from 10:00am to 12:00am of the day ? (Still I will be free in the afternoon, if you could introduce some persons on animal or microbial systems biology, I would most appreciate.) Looking for hearing from you. With best regards, Toru YAO Advisor, RIKEN On Fri, 01 Jun 2007 09:15:45 +0900 yao <yao(a)riken.jp> wrote: > Dear Prof. Dirk Inze; > > Thank you very much for your quick reply on the acceptance > of my visit in July. > > I will visit you on July 20(Fri). > > Dear Prof. Martin Kuiper; > > As Prof.Inze introduced you, I am very happy to visit you > on July 20(Fri). > > I am very much interested with the Computational Biology, > Bioinformatics and Systems Biology, and would like to hear > your activities and prospects in these fields. > > If possible, please introduce some appropriate persons of > these fields on animals or model organisms. > > I also wanat to visit experimental sites. > > I will be free whole day of July 20, but I don't want to > disturbe so much your valuable time. Please arrange for > separate short time spans. > > I will stay at a hotel in Brussell from 19 to 21. > > Looking forward to hearing from you. > > With best regards, > Toru YAO > > > On Thu, 31 May 2007 12:45:40 +0200 > "Dirk Inze" <dirk.inze(a)psb.UGent.be> wrote: > > > Dear Prof Yao, > > I also enjoyed our brief meeting in RIKEN PSC. You are > > most welcome to visit VIB-Plant Systems Biology on both Thursday > > 19th and Friday 20th July. My senior colleague, Prof Martin Kuiper, > > head of the computational biology group, will be in charge of you > > visit. Please establish direct contacts with Dr Kuiper > > (makui(a)psb.ugent.be) Both Prof Yves Van de Peer (head of the > > bioinformatics group) and myself are not available on Thursday but > > we will be able to meet and discuss with you on Friday. > > I look forward to meet you in July in Ghent. > > > > With kind regards > > Dirk Inze > > -------------------------------------------------------------------- > > ---- > > -- > > Prof.Dr.Dirk Inze > > Science Director > > VIB Department of Plant Systems Biology, UGent > > > > Technologiepark 927 > > 9052 Ghent, Belgium > > tel: +32-9-331.38.06 fax: +32-9-331.38.09 > > dirk.inze(a)psb.ugent.be http://www.psb.ugent.be > > -------------------------------------------------------------------- > > ---- > > -- > > > > > > > > -----Original Message----- > > From: yao [mailto:yao@riken.jp] > > Sent: donderdag 31 mei 2007 11:46 > > To: diinz(a)psb.UGent.be > > Subject: My visit you in July-- Toru YAO/RIKEN > > > > Dear Prof.Dirk Inze; > > > > It was a good meeting with you at RIKEN here the day before > > yesterday on May 28. > > > > As I said at that time, I would like to visit you at Gent > > either on July 20(Fri) or 19(Thu), if you were acceptable. > > > > I am sorry that my available dates are only above two days. > > I will attend to the ISMB/ECCB in Viena on 21-25 July, and > > leave Japan on July 18 to arrive at Brussell in the evening > > on July 18. > > > > My purpose of this visit is to hear your activities and > > pespectives on the Systems Biology of Plants. > > > > If possible, please introduce the persons on the Systems > > Bilogy of Animals or Model Organisms. > > > > Let me introduce briefly myself. > > I am working as the advisor on Bioinformatics and Systems > > Biology at Genomic Sciences Center of RIKEN for nine years > > from 1998. > > Recently, I am very much interested with the progress of the > > Systems Bilogy in various fields not only for the analyses of > > fundamental biological processes, but also for the applications > > to medical, environmental fields. > > > > I have been talking with Drs.Shinozaki,Saito,Matsui,Deguchi,Seki > > et al on this problem several times. > > > > Anyway, would you please find a short time for me and recommend > > some other appropriate persons ? > > > > Looking forward to hearing from you by return. > > > > With best regards, > > Toru YAO > > yao(a)riken.jp > > 81-45-503-9295 > > RIKEN Yokohama > > > > I will attach my papers and intro. > > > > > > -- > yao <yao(a)postman.riken.go.jp> -- yao <yao(a)postman.riken.go.jp> -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://www.psb.ugent.be/bioinformatics/

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[Beg-sysbiol] we zouden dan ook eens moeten samenzitten als Greg hier is, i.v.m. wat hij gaat doen denk ik ... netwerken en gedupliceerde genen (steven?)
by Yves Van de Peer 19 Jun '07

19 Jun '07

-- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://www.psb.ugent.be/bioinformatics/

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[Beg-sysbiol] paper
by Eric Bonnet 18 Jun '07

18 Jun '07

insightful & elegant paper about network motifs involving microRNAs. Probably one of the first serious "sysbiol" approach integrating microRNAs. Eric

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[Beg-sysbiol] module code
by Steven Maere 18 Jun '07

18 Jun '07

Hi, I'm sending you the adjusted module class (from my ENIGMA software), contains corrected code for module visualization (solved scrambling of data in separate leaves) as well as for eps figures, amongst others. The bayesian stuff is not in this class (results didn't make sense for my problem), so probably the best thing to do is to cut and paste relevant parts of the code in your code. Some other stuff that you might decide (not) to use: yellow-blue color scheme, condition labels, clustering of genes and/or conditions with cosine correlation coefficient, definition of extra leaf that groups all leaves with condition sets smaller than 3, which are excluded from the regulation program (too few datapoints to determine sensible regulators), prioritization of potential regulators based on whether their binding site is overrepresented in the module (provided you have chip data), extra visualization of overrepresented TFs, overrepresented GO categories and links to other modules. It is very possible that for some of this stuff to work, you need adjustments in other classes. Ask me to send them to you, or wait till the ENIGMA code is released (1 week). Don't trust the calculatePCCmap() function, there might be something wrong with it. Best, Steven -- ================================================================== Steven Maere, PhD Dept. of Plant Systems Biology Bioinformatics & Evolutionary Genomics research group VIB / Ghent University Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3810 fax: +32 9 331 3809 email: stmae(a)psb.UGent.be http://www.psb.UGent.be http://bioinformatics.psb.ugent.be/ ================================================================== /* ENIGMA - Expression Network Inference and Gene Module Analysis Copyright (C) 2007 Flanders Interuniversitary Intsitute for Biotechnology (VIB) This source code is freely distributed under the terms of the GNU General Public License. See the files COPYRIGHT and LICENSE for details. Written by Steven Maere */ /* LeMoNe - a software to build module networks from expression data Copyright (C) 2005-2006 Flanders Interuniversitary Intsitute for Biotechnology (VIB) This source code is freely distributed under the terms of the GNU General Public License. See the files COPYRIGHT and LICENSE for details. Written by Eric Bonnet, Steven Maere, Tom Michoel, Yvan Saeys */ package enigma; import java.util.*; import java.util.List; import java.io.*; import java.awt.*; import java.awt.image.*; import java.awt.font.*; import java.awt.geom.*; import javax.imageio.*; import javax.swing.*; import net.sf.epsgraphics.*; import cern.jet.stat.*; import cern.colt.list.*; import cytoscape.data.annotation.OntologyTerm; public class Module extends JComponent { // FIELDS public ModuleNetwork moduleNetwork; public int number; public String name; public HashSet<Gene> Parents = new HashSet<Gene>(); public HashSet<Gene> Genes = new HashSet<Gene>(); public ArrayList<Gene> ordenedGenes = new ArrayList<Gene>(); public HashMap<Gene,Double> TFs = new HashMap<Gene,Double>(); public LinkedHashMap<OntologyTerm,Double> GO = new LinkedHashMap<OntologyTerm,Double>(); public HashMap<Condition,Double> Conditions = new HashMap<Condition,Double>(); public ArrayList<Condition> nonTreeConditions = new ArrayList<Condition>(); public HashMap<Integer,Condition> numberedConditions = new HashMap<Integer,Condition>(); public TreeNode regressionTree; // root node; this is the regulation program public TreeNode rightmostNode; // rightmost leaf node (for attaching gene labels in module picture) public LinkedHashSet<Module> modLinks = new LinkedHashSet<Module>(); public HashMap<Gene,HashMap<Gene,Double>> distMap; public HashMap<Condition,HashMap<Condition,Double>> condDistMap; public BingoResults bingoResults ; public boolean dist = true; //true to use distances to compare genes, false to use correlations // CONSTRUCTOR public Module() { } public Module(int number) { this.number = number; this.regressionTree = new TreeNode(); } public Module(String name, int number, HashSet Genes){ this.name = name; this.number = number; for(Object j: Genes){ this.Genes.add((Gene) j); this.ordenedGenes.add((Gene) j); } } // METHODS /* * This builds a full hierarchical clustering tree of the data in the * module, which can then be converted in a regulation program tree. * * Usage of TreeNode and LeafDistribution is somewhat different than for * regressionTree: - testGene and splitValue are not set on internal nodes - * internal nodes have a LeafDistribution as well, containing the statistics * of all leaves (=experiments) below it. The data given as input is the * full data matrix, but condSet may limit the set of experiments to be * clustered */ public void addGene(Gene g){ Genes.add(g); ordenedGenes.add(g); } public TreeNode avLinkHierarchicalClustering(TreeNode t) { if(!t.nodeStatus.equals("leaf")){ TreeNode bestTree = new TreeNode(); //calculateCondEuclDistMap(); calculateCondCosineCorMap(); // initialize treeList with the leaves of t ArrayList<TreeNode> treeList = new ArrayList<TreeNode>(); ArrayList<TreeNode> tmp = new ArrayList<TreeNode>(); t.gatherLeafList(treeList); t.gatherLeafList(tmp); //remove leafs with less than 3 conditions and put them aside... for(TreeNode tr: tmp){ if(tr.leafDistribution.condSet.size() < 3){ treeList.remove(tr); for(Integer c: tr.leafDistribution.condSet){ nonTreeConditions.add(numberedConditions.get(c)); } } } ArrayList<TreeNode> pairTreeList = new ArrayList<TreeNode>(); if(treeList.size() > 1){ // initialize list of pairwise merges for (int i = 0; i < treeList.size(); i++){ for (int j = 0; j < i; j++) { TreeNode tree = new TreeNode(); tree.nodeStatus = "internal"; tree.compareMeans = 2; tree.leftChild = treeList.get(i); tree.rightChild = treeList.get(j); tree.module = this; for (int s = 0; s < 3; s++){ tree.leafDistribution.statistics[s] = treeList.get(i).leafDistribution.statistics[s] + treeList.get(j).leafDistribution.statistics[s]; } for (int c : tree.leftChild.leafDistribution.condSet) tree.leafDistribution.condSet.add(c); for (int c : tree.rightChild.leafDistribution.condSet) tree.leafDistribution.condSet.add(c); pairTreeList.add(tree); } } // merge trees in treeList until one tree is left boolean keep; int cnt; bestTree = new TreeNode(); while (treeList.size() > 1) { // find the optimal pair tree bestTree = Collections.min(pairTreeList); // remove children of bestTree from treeList; bestTree will be added at the end treeList.remove(bestTree.leftChild); treeList.remove(bestTree.rightChild); // loop over the pair list and remove trees whose condSet intersects // with the condSet of the highest scoring tree, including the highest one // itself Iterator<TreeNode> it = pairTreeList.iterator(); while (it.hasNext()) { TreeNode tree = it.next(); keep = true; cnt = 0; while (keep & cnt < tree.leafDistribution.condSet.size()) { if (bestTree.leafDistribution.condSet.contains(tree.leafDistribution.condSet.get(cnt))){ keep = false; } cnt++; } if (!keep){ it.remove(); } } // add new trees which merge the bestTree with the other trees in // treeList; Iterator<TreeNode> it2 = treeList.iterator(); while (it2.hasNext()) { TreeNode ittree = it2.next(); TreeNode tree = new TreeNode(); tree.nodeStatus = "internal"; tree.compareMeans = 2; tree.leftChild = ittree; tree.rightChild = bestTree; tree.module = this; for (int s = 0; s < 3; s++){ tree.leafDistribution.statistics[s] = tree.leftChild.leafDistribution.statistics[s] + tree.rightChild.leafDistribution.statistics[s]; } for (Integer c : tree.leftChild.leafDistribution.condSet) tree.leafDistribution.condSet.add(c); for (Integer c : bestTree.leafDistribution.condSet) tree.leafDistribution.condSet.add(c); pairTreeList.add(tree); } // add bestTree again to treeList treeList.add(bestTree); // set bestTree as parent of its children bestTree.leftChild.parentNode = bestTree; bestTree.rightChild.parentNode = bestTree; } } else{ //no internal nodes, make one leaf node bestTree = new TreeNode(); for(TreeNode tr: treeList){ bestTree.leafDistribution.condSet.addAll(tr.leafDistribution.condSet); } for(Condition c: this.nonTreeConditions){ bestTree.leafDistribution.condSet.add(c.number); } bestTree.statistics(this.moduleNetwork.data,this.Genes); bestTree.module = this; } // 1 tree left, this is the one return bestTree; } else{ return t; } } //means-based average linkage hierachical clustering of conditions public TreeNode meansAvLinkHierarchicalClustering(TreeNode t) { if(!t.nodeStatus.equals("leaf")){ TreeNode bestTree = new TreeNode(); // initialize treeList with the leaves inferred from hierarchical clustering ArrayList<TreeNode> treeList = new ArrayList<TreeNode>(); ArrayList<TreeNode> tmp = new ArrayList<TreeNode>(); t.gatherLeafList(treeList); t.gatherLeafList(tmp); //remove leafs with less than 3 conditions and put them aside... for(TreeNode tr: tmp){ if(tr.leafDistribution.condSet.size() < 3){ treeList.remove(tr); for(Integer c: tr.leafDistribution.condSet){ nonTreeConditions.add(numberedConditions.get(c)); } } } ArrayList<TreeNode> pairTreeList = new ArrayList<TreeNode>(); if(treeList.size() > 1){ // initialize list of pairwise merges for (int i = 0; i < treeList.size(); i++){ for (int j = 0; j < i; j++) { TreeNode tree = new TreeNode(); tree.nodeStatus = "internal"; tree.compareMeans = 1; tree.leftChild = treeList.get(i); tree.rightChild = treeList.get(j); for (int s = 0; s < 3; s++){ tree.leafDistribution.statistics[s] = treeList.get(i).leafDistribution.statistics[s] + treeList.get(j).leafDistribution.statistics[s]; } //tree.leafDistribution.bayesianScore(); for (int c : tree.leftChild.leafDistribution.condSet) tree.leafDistribution.condSet.add(c); for (int c : tree.rightChild.leafDistribution.condSet) tree.leafDistribution.condSet.add(c); //tree.leafDistribution.bayesianScore(); pairTreeList.add(tree); } } // merge trees in treeList until one tree is left boolean keep; int cnt; while (treeList.size() > 1) { // find the pair tree with the smallest difference in mean expression (compareMeans = true) bestTree = Collections.min(pairTreeList); // remove children of bestTree from treeList; bestTree will be added at the end treeList.remove(bestTree.leftChild); treeList.remove(bestTree.rightChild); // loop over the pair list and remove trees whose condSet intersects // with the condSet of the highest scoring tree, including the highest one // itself Iterator<TreeNode> it = pairTreeList.iterator(); while (it.hasNext()) { TreeNode tree = it.next(); keep = true; cnt = 0; while (keep & cnt < tree.leafDistribution.condSet.size()) { if (bestTree.leafDistribution.condSet .contains(tree.leafDistribution.condSet.get(cnt))) keep = false; cnt++; } if (!keep) it.remove(); } // add new trees which merge the bestTree with the other trees in // treeList; Iterator<TreeNode> it2 = treeList.iterator(); while (it2.hasNext()) { TreeNode ittree = it2.next(); TreeNode tree = new TreeNode(); tree.nodeStatus = "internal"; tree.compareMeans = 1; tree.leftChild = ittree; tree.rightChild = bestTree; for (int s = 0; s < 3; s++){ tree.leafDistribution.statistics[s] = tree.leftChild.leafDistribution.statistics[s] + tree.rightChild.leafDistribution.statistics[s]; } //tree.leafDistribution.bayesianScore(); for (Integer c : tree.leftChild.leafDistribution.condSet) tree.leafDistribution.condSet.add(c); for (Integer c : bestTree.leafDistribution.condSet) tree.leafDistribution.condSet.add(c); //tree.leafDistribution.bayesianScore(); pairTreeList.add(tree); } // add bestTree again to treeList treeList.add(bestTree); // set bestTree as parent of its children bestTree.leftChild.parentNode = bestTree; bestTree.rightChild.parentNode = bestTree; // System.out.println(bestTree.postProb); } } else{ //no internal nodes, make one leaf node bestTree = new TreeNode(); for(TreeNode tr: treeList){ bestTree.leafDistribution.condSet.addAll(tr.leafDistribution.condSet); } for(Condition c: this.nonTreeConditions){ bestTree.leafDistribution.condSet.add(c.number); } bestTree.statistics(this.moduleNetwork.data,this.Genes); bestTree.module = this; } // 1 tree left, this is the one return bestTree; } else{ return t; } } public TreeNode avLinkHierarchicalClustering(ArrayList<Integer> condSet, double data[][]) { if(condSet.size() > 1){ //calculateCondEuclDistMap(); calculateCondCosineCorMap(); ArrayList<TreeNode> treeList = new ArrayList<TreeNode>(); // initialize treeList with just the bare leaves for (int i : condSet) { TreeNode tree = new TreeNode(); tree.nodeStatus = "leaf"; tree.module = this; tree.leafDistribution.condSet.add(i); for (Gene gene : this.Genes) if (!Double.isNaN(data[gene.number][i])) { tree.leafDistribution.statistics[0]++; tree.leafDistribution.statistics[1] += data[gene.number][i]; tree.leafDistribution.statistics[2] += Math.pow(data[gene.number][i], 2); } treeList.add(tree); } ArrayList<TreeNode> pairTreeList = new ArrayList<TreeNode>(); // initialize list of pairwise merges for (int i = 0; i < treeList.size(); i++){ for (int j = 0; j < i; j++) { TreeNode tree = new TreeNode(); tree.nodeStatus = "internal"; tree.compareMeans = 2; tree.leftChild = treeList.get(i); tree.rightChild = treeList.get(j); tree.module = this; for (int s = 0; s < 3; s++){ tree.leafDistribution.statistics[s] = treeList.get(i).leafDistribution.statistics[s] + treeList.get(j).leafDistribution.statistics[s]; } for (int c : tree.leftChild.leafDistribution.condSet) tree.leafDistribution.condSet.add(c); for (int c : tree.rightChild.leafDistribution.condSet) tree.leafDistribution.condSet.add(c); pairTreeList.add(tree); } } // merge trees in treeList until one tree is left boolean keep; int cnt; TreeNode bestTree = new TreeNode(); while (treeList.size() > 1) { // find the optimal pair tree bestTree = Collections.min(pairTreeList); // remove children of bestTree from treeList; bestTree will be added at the end treeList.remove(bestTree.leftChild); treeList.remove(bestTree.rightChild); // loop over the pair list and remove trees whose condSet intersects // with the condSet of the highest scoring tree, including the highest one // itself Iterator<TreeNode> it = pairTreeList.iterator(); while (it.hasNext()) { TreeNode tree = it.next(); keep = true; cnt = 0; while (keep & cnt < tree.leafDistribution.condSet.size()) { if (bestTree.leafDistribution.condSet.contains(tree.leafDistribution.condSet.get(cnt))){ keep = false; } cnt++; } if (!keep){ it.remove(); } } // add new trees which merge the bestTree with the other trees in // treeList; Iterator<TreeNode> it2 = treeList.iterator(); while (it2.hasNext()) { TreeNode ittree = it2.next(); TreeNode tree = new TreeNode(); tree.nodeStatus = "internal"; tree.compareMeans = 2; tree.leftChild = ittree; tree.rightChild = bestTree; tree.module = this; for (int s = 0; s < 3; s++){ tree.leafDistribution.statistics[s] = tree.leftChild.leafDistribution.statistics[s] + tree.rightChild.leafDistribution.statistics[s]; } for (Integer c : tree.leftChild.leafDistribution.condSet) tree.leafDistribution.condSet.add(c); for (Integer c : bestTree.leafDistribution.condSet) tree.leafDistribution.condSet.add(c); pairTreeList.add(tree); } // add bestTree again to treeList treeList.add(bestTree); // set bestTree as parent of its children bestTree.leftChild.parentNode = bestTree; bestTree.rightChild.parentNode = bestTree; } // 1 tree left, this is the one return bestTree; } else{ //tree with a single leaf TreeNode bestTree = new TreeNode() ; bestTree.nodeStatus = "leaf"; bestTree.module = this; for(Integer i:condSet){ bestTree.leafDistribution.condSet.add(i); for (Gene gene : this.Genes){ if (!Double.isNaN(data[gene.number][i])) { bestTree.leafDistribution.statistics[0]++; bestTree.leafDistribution.statistics[1] += data[gene.number][i]; bestTree.leafDistribution.statistics[2] += Math.pow(data[gene.number][i], 2); } } } return bestTree; } } public void calculatePCCmap(){ this.dist = false; distMap = new HashMap<Gene,HashMap<Gene,Double>>(); for(Gene t1:this.Genes){ for(Gene t2:this.Genes){ double[] exp1 = new double[this.Conditions.size()]; double[] exp2 = new double[this.Conditions.size()]; int count = 0 ; for(int i=0; i < this.moduleNetwork.data[t1.number].length;i++){ if (this.numberedConditions.keySet().contains(i)){ exp1[count] = this.moduleNetwork.data[t1.number][i]; exp2[count] = this.moduleNetwork.data[t2.number][i]; count++; } } DoubleArrayList a1 = new DoubleArrayList(exp1); DoubleArrayList a2 = new DoubleArrayList(exp2); double v1; double v2; if(a1.size() > 1){ v1 = cern.jet.stat.Descriptive.sampleStandardDeviation(a1.size(), cern.jet.stat.Descriptive.sampleVariance(a1,cern.jet.stat.Descriptive.mean(a1))); v2 = cern.jet.stat.Descriptive.sampleStandardDeviation(a2.size(), cern.jet.stat.Descriptive.sampleVariance(a2,cern.jet.stat.Descriptive.mean(a2))); double pcc = cern.jet.stat.Descriptive.correlation(a1,v1,a2,v2); if(!distMap.containsKey(t1)){ distMap.put(t1,new HashMap<Gene,Double>()); } distMap.get(t1).put(t2,new Double(pcc)); } else{ //correlation between genes for single exp doesn't make much sense if(!distMap.containsKey(t1)){ distMap.put(t1,new HashMap<Gene,Double>()); } distMap.get(t1).put(t2,new Double(0)); } } } } public void calculateEuclDistMap(){ this.dist = true; distMap = new HashMap<Gene,HashMap<Gene,Double>>(); for(Gene t1:this.Genes){ for(Gene t2:this.Genes){ double[] exp1 = new double[this.Conditions.size()]; double[] exp2 = new double[this.Conditions.size()]; int count = 0 ; for(int i=0; i < this.moduleNetwork.data[t1.number].length;i++){ if (this.numberedConditions.keySet().contains(i)){ exp1[count] = this.moduleNetwork.data[t1.number][i]; exp2[count] = this.moduleNetwork.data[t2.number][i]; count++; } } double dist = 0; for(int i = 0; i < exp1.length; i++){ if(!Double.isNaN(exp1[i]) && !Double.isNaN(exp2[i])){ dist += Math.pow(exp1[i]-exp2[i],2); } } dist = Math.sqrt(dist); if(!distMap.containsKey(t1)){ distMap.put(t1,new HashMap<Gene,Double>()); } distMap.get(t1).put(t2,new Double(dist)); } } } public void calculateCosineCorMap(){ this.dist = false; distMap = new HashMap<Gene,HashMap<Gene,Double>>(); for(Gene t1:this.Genes){ for(Gene t2:this.Genes){ double[] exp1 = new double[this.Conditions.size()]; double[] exp2 = new double[this.Conditions.size()]; int count = 0 ; for(int i=0; i < this.moduleNetwork.data[t1.number].length;i++){ if (this.numberedConditions.keySet().contains(i)){ exp1[count] = this.moduleNetwork.data[t1.number][i]; exp2[count] = this.moduleNetwork.data[t2.number][i]; count++; } } double corr = 0; double sum1 = 0; double sum2 = 0; for(int i = 0; i < exp1.length; i++){ if(!Double.isNaN(exp1[i]) && !Double.isNaN(exp2[i])){ corr += exp1[i]*exp2[i]; sum1 += Math.pow(exp1[i],2); sum2 += Math.pow(exp2[i],2); } } if((sum1 != 0) && (sum2 != 0) && (corr != Double.NaN)){ corr = corr / (Math.sqrt(sum1)*Math.sqrt(sum2)); } else{ System.out.println("Error in calculating cosine correlation for module " + this.name); } if(!distMap.containsKey(t1)){ distMap.put(t1,new HashMap<Gene,Double>()); } distMap.get(t1).put(t2,new Double(corr)); } } } public void calculateCondEuclDistMap(){ condDistMap = new HashMap<Condition,HashMap<Condition,Double>>(); HashMap<Integer,Gene> numberedGenes = new HashMap<Integer,Gene>(); for(Gene g: this.Genes){ numberedGenes.put(g.number,g); } for(Condition t1:this.Conditions.keySet()){ for(Condition t2:this.Conditions.keySet()){ double[] exp1 = new double[this.Genes.size()]; double[] exp2 = new double[this.Genes.size()]; int count = 0 ; for(int i=0; i < this.moduleNetwork.data.length;i++){ if (numberedGenes.keySet().contains(i)){ exp1[count] = this.moduleNetwork.data[i][t1.number]; exp2[count] = this.moduleNetwork.data[i][t2.number]; count++; } } double dist = 0; for(int i = 0; i < exp1.length; i++){ if(!Double.isNaN(exp1[i]) && !Double.isNaN(exp2[i])){ dist += Math.pow(exp1[i]-exp2[i],2); } } dist = Math.sqrt(dist); if(!condDistMap.containsKey(t1)){ condDistMap.put(t1,new HashMap<Condition,Double>()); } condDistMap.get(t1).put(t2,new Double(dist)); } } } public void calculateCondCosineCorMap(){ condDistMap = new HashMap<Condition,HashMap<Condition,Double>>(); HashMap<Integer,Gene> numberedGenes = new HashMap<Integer,Gene>(); for(Gene g: this.Genes){ numberedGenes.put(g.number,g); } for(Condition t1:this.Conditions.keySet()){ for(Condition t2:this.Conditions.keySet()){ double[] exp1 = new double[this.Genes.size()]; double[] exp2 = new double[this.Genes.size()]; int count = 0 ; for(int i=0; i < this.moduleNetwork.data.length;i++){ if (numberedGenes.keySet().contains(i)){ exp1[count] = this.moduleNetwork.data[i][t1.number]; exp2[count] = this.moduleNetwork.data[i][t2.number]; count++; } } double corr = 0; double sum1 = 0; double sum2 = 0; for(int i = 0; i < exp1.length; i++){ if(!Double.isNaN(exp1[i]) && !Double.isNaN(exp2[i])){ corr += exp1[i]*exp2[i]; sum1 += Math.pow(exp1[i],2); sum2 += Math.pow(exp2[i],2); } } if((sum1 != 0) && (sum2 != 0) && (corr != Double.NaN)){ corr = corr / (Math.sqrt(sum1)*Math.sqrt(sum2)); } else{ System.out.println("Error in calculating cosine correlation for module " + this.name); } if(!condDistMap.containsKey(t1)){ condDistMap.put(t1,new HashMap<Condition,Double>()); } condDistMap.get(t1).put(t2,new Double(corr)); } } } public void calculateMatchSimMap(double pThres){ this.dist = false; distMap = new HashMap<Gene,HashMap<Gene,Double>>(); for(Gene t1:this.Genes){ for(Gene t2:this.Genes){ double[] exp1 = new double[this.Conditions.size()]; double[] exp2 = new double[this.Conditions.size()]; double[] p1 = new double[this.Conditions.size()]; double[] p2 = new double[this.Conditions.size()]; int count = 0 ; for(int i=0; i < this.moduleNetwork.data[t1.number].length;i++){ if (this.numberedConditions.keySet().contains(i)){ exp1[count] = this.moduleNetwork.data[t1.number][i]; exp2[count] = this.moduleNetwork.data[t2.number][i]; p1[count] = this.moduleNetwork.pvals[t1.number][i]; p2[count] = this.moduleNetwork.pvals[t2.number][i]; count++; } } double match = 0; for(int i = 0; i < exp1.length; i++){ if((p1[i]<pThres)&&(p2[i]<pThres)&&(exp1[i]>0)&&(exp2[i]>0)){ match++; } else if((p1[i]<pThres)&&(p2[i]<pThres)&&(exp1[i]<0)&&(exp2[i]<0)){ match++; } } if(!distMap.containsKey(t1)){ distMap.put(t1,new HashMap<Gene,Double>()); } distMap.get(t1).put(t2,new Double(match)); } } } public GeneTree clusterGenes(){ // average linkage clustering of gene profiles // initialize list of pairwise merges //this.calculatePCCmap(); //this.calculateEuclDistMap(); //this.calculateMatchSimMap(0.01); this.calculateCosineCorMap(); ArrayList<GeneTree> treeList = new ArrayList<GeneTree>(); ArrayList<GeneTree> pairTreeList = new ArrayList<GeneTree>(); int ind = 0; for (Gene i: Genes){ treeList.add(ind,new GeneTree(i,this,dist)); ind++; } for (int i = 0; i < treeList.size(); i++){ for (int j = 0; j < i; j++) { HashSet<Gene> geneList = new HashSet<Gene>(); geneList.addAll(treeList.get(i).Genes); geneList.addAll(treeList.get(j).Genes); GeneTree tree = new GeneTree(geneList,this,treeList.get(i),treeList.get(j),dist); pairTreeList.add(tree); } } // merge trees in treeList until one tree is left boolean keep; int cnt; GeneTree bestTree = new GeneTree(); while (treeList.size() > 1) { // find the pair tree with the smallest difference in mean expression (compareMeans = true) bestTree = Collections.min(pairTreeList); // remove children of bestTree from treeList; bestTree will be added at the end treeList.remove(bestTree.leftChild); treeList.remove(bestTree.rightChild); // loop over the pair list and remove trees whose condSet intersects // with the condSet of the highest scoring tree, including the highest one // itself Iterator<GeneTree> it = pairTreeList.iterator(); while (it.hasNext()) { GeneTree tree = it.next(); keep = true; for(Gene g:tree.Genes) { if (bestTree.Genes.contains(g)){ keep = false; } } if (!keep){ it.remove(); } } // add new trees which merge the bestTree with the other trees in // treeList; Iterator<GeneTree> it2 = treeList.iterator(); while (it2.hasNext()) { GeneTree ittree = it2.next(); HashSet<Gene> geneList = new HashSet<Gene>(); geneList.addAll(bestTree.Genes); geneList.addAll(ittree.Genes); GeneTree tree = new GeneTree(geneList,this,ittree,bestTree,dist); pairTreeList.add(tree); } // add bestTree again to treeList treeList.add(bestTree); // set bestTree as parent of its children bestTree.leftChild.parentNode = bestTree; bestTree.rightChild.parentNode = bestTree; // System.out.println(bestTree.postProb); } // 1 tree left, this is the one // construct ordened gene list by depth-first search of bestTree this.ordenedGenes = new ArrayList<Gene>(); ArrayList<GeneTree> ordenedLeafs = new ArrayList<GeneTree>() ; bestTree.gatherLeafList(ordenedLeafs); for(int i = 0; i < ordenedLeafs.size(); i++){ this.ordenedGenes.addAll(ordenedLeafs.get(i).Genes); } return bestTree; } // draw module public void draw() { // scale factor int sc = 4; // coordinates of origin int x0 = 15; int y0 = 10; // tree step height int h = 18; // figure width String modName = "Module " + this.number + " : " + this.name; int width = Math.max(3 * x0 + 2*this.Conditions.size() + 5 + 2*this.TFs.keySet().size() + 2 + 2*this.GO.keySet().size() + 2 + 2*this.modLinks.size(),2*modName.length()+10); int height; int x = x0; int ybase = y0; //figure height //find largest GO term BufferedImage tmpIm = new BufferedImage(200, 200,BufferedImage.TYPE_INT_BGR); Graphics2D tmp = tmpIm.createGraphics(); tmp.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); tmp.scale(sc, sc); FontRenderContext frc = tmp.getFontRenderContext(); int goHeight = 0; for(OntologyTerm go: GO.keySet()){ int a = Math.round((float) (new Font("SansSerif", Font.BOLD, 2).getStringBounds(go.getName(), frc).getWidth())); if(a > goHeight){ goHeight = a; } } //find largest Gene name int nameHeight = 0; for(Gene g : this.Genes){ //at 30 degree angle... int a = Math.round((float) (new Font("SansSerif", Font.BOLD, 2).getStringBounds(g.name, frc).getWidth() * Math.sqrt(3)/2.0)); if(a > goHeight){ nameHeight = a; } } int treeHeight = (h + 4) * (this.regressionTree.treeDepth() + 1); if(goHeight > treeHeight){ treeHeight = goHeight; } //set dimensions ybase = y0 + treeHeight; height = ybase + 2 * y0 + this.Genes.size()*2 + nameHeight; if (this.regressionTree.nodeStatus.equals("leaf")){ // no tree this.rightmostNode = this.regressionTree; } else { //find rightmost node to attach non-tree conditions and gene labels TreeNode tempNode = this.regressionTree ; while(tempNode.rightChild.nodeStatus.equals("internal")){tempNode = tempNode.rightChild;} this.rightmostNode = tempNode; // coordinates of root x = x0 + 2*this.regressionTree.leftChild.leafDistribution.condSet.size(); } BufferedImage image = new BufferedImage(sc * width, sc * height, BufferedImage.TYPE_INT_BGR); Graphics2D g2; g2 = image.createGraphics(); g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); g2.scale(sc, sc); g2.setStroke(new BasicStroke(0.5F)); if (this.regressionTree.nodeStatus.equals("leaf")) { // no tree g2.setPaint(Color.white); g2.fillRect(0, 0, width, height); // draw data g2.setFont(new Font("SansSerif", Font.BOLD, 4)); g2.setPaint(Color.black); g2.drawString(modName , width/2 - 2*modName.length()/2, new Float(y0/2)); draw1leaf(x0, ybase, this.moduleNetwork.data, g2); } else { g2.setPaint(Color.white); g2.fillRect(0, 0, width, height); // draw regression tree g2.setFont(new Font("SansSerif", Font.BOLD, 4)); g2.setPaint(Color.black); g2.drawString(modName , width/2 - 2*modName.length()/2, new Float(y0/2)); drawnode(this.regressionTree, x, y0, h, ybase,this.moduleNetwork.data, g2); } String filename = "module" + this.number + ".png"; File outFile = new File(this.moduleNetwork.dataDir, filename); try { ImageIO.write(image, "png", outFile); } catch (IOException e) { return; } } // draw eps fig public void drawEps() { // scale factor int sc = 4; // coordinates of origin int x0 = 15; int y0 = 10; // tree step height int h = 18; // figure width int width = 3 * x0 + 2*this.Conditions.size() + 5 + 2*this.TFs.keySet().size()+ 2 + 2*this.GO.keySet().size() + 2 + 2*this.modLinks.size(); int height; int x = x0; int ybase = y0; String modName = "Module " + this.number + " : " + this.name; //figure height //find largest GO term BufferedImage tmpIm = new BufferedImage(200, 200,BufferedImage.TYPE_INT_BGR); Graphics2D tmp = tmpIm.createGraphics(); tmp.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); tmp.scale(sc, sc); FontRenderContext frc = tmp.getFontRenderContext(); int goHeight = 0; for(OntologyTerm go: GO.keySet()){ int a = Math.round((float) (new Font("SansSerif", Font.BOLD, 2).getStringBounds(go.getName(), frc).getWidth())); if(a > goHeight){ goHeight = a; } } //find largest Gene name int nameHeight = 0; for(Gene g : this.Genes){ //at 30 degree angle... int a = Math.round((float) (new Font("SansSerif", Font.BOLD, 2).getStringBounds(g.name, frc).getWidth() * Math.sqrt(3)/2.0)); if(a > goHeight){ nameHeight = a; } } int treeHeight = (h + 4) * (this.regressionTree.treeDepth() + 1); if(goHeight > treeHeight){ treeHeight = goHeight; } //set dimensions ybase = y0 + treeHeight; height = ybase + 2 * y0 + this.Genes.size()*2 + nameHeight; if (this.regressionTree.nodeStatus.equals("leaf")){ // no tree this.rightmostNode = this.regressionTree; } else { //find rightmost node to attach non-tree conditions and gene labels TreeNode tempNode = this.regressionTree ; while(tempNode.rightChild.nodeStatus.equals("internal")){tempNode = tempNode.rightChild;} this.rightmostNode = tempNode; // coordinates of root x = x0 + 2*this.regressionTree.leftChild.leafDistribution.condSet.size(); } try{ EpsGraphics g2 = new EpsGraphics("module" + this.number + ".eps", new FileOutputStream(new File(this.moduleNetwork.dataDir,"module" + this.number + ".eps")),0,0,sc*width,sc*height,ColorMode.COLOR_CMYK); g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); g2.scale(sc, sc); g2.setStroke(new BasicStroke(0.5F)); if (this.regressionTree.nodeStatus.equals("leaf")) { // no tree g2.setPaint(Color.white); g2.fillRect(0, 0, width, height); // draw data g2.setFont(new Font("SansSerif", Font.BOLD, 4)); g2.setPaint(Color.black); g2.drawString(modName , width/2 - 2*modName.length()/2, new Float(y0/2)); draw1leaf(x0, ybase, this.moduleNetwork.data, g2); } else { g2.setPaint(Color.white); g2.fillRect(0, 0, width, height); // draw regression tree g2.setFont(new Font("SansSerif", Font.BOLD, 4)); g2.setPaint(Color.black); g2.drawString(modName , width/2 - 2*modName.length()/2, new Float(y0/2)); drawnode(this.regressionTree, x, y0, h, ybase,this.moduleNetwork.data, g2); } g2.close(); } catch(Exception e){ System.out.println(e.toString()); } } // convert expression value to color public Color data2Color(Gene gene, double data) { Color col; float blueperc, yellowperc; blueperc = new Float(gene.upProb(data,this.moduleNetwork.dataMean,this.moduleNetwork.dataSigma)); yellowperc = new Float(gene.downProb(data,this.moduleNetwork.dataMean,this.moduleNetwork.dataSigma)); col = new Color(yellowperc, yellowperc, blueperc); return col; } // draw a node public void drawnode(TreeNode node, int x, int y, int h, int ybase, double[][] data, Graphics2D g) { // input: // (x,y): start coordinates, h: height of vertical node line, // ybase: baseline where leaves begin // data: expression data // g: graphics in which node is drawn if (node.nodeStatus.equals("internal")) { // where to start drawing regulator expression values int x1 = x - 2*node.leftChild.leafDistribution.condSet.size(); // draw regulator expression values left of split point for (int m = 0; m < node.leftChild.leafDistribution.condSet.size(); m++) { int exp = node.leftChild.leafDistribution.condSet.get(m); if (!Double.isNaN(data[node.testGene.number][exp])) { // convert data value to color Color col = data2Color(node.testGene,data[node.testGene.number][exp]); g.setPaint(col); } else // missing value g.setPaint(Color.white); g.fillRect(x1 + 2*m, y + h - 4, 2, 1); } // draw regulator expression values right of split point for (int m = 0; m < node.rightChild.leafDistribution.condSet.size(); m++) { int exp = node.rightChild.leafDistribution.condSet.get(m); if (!Double.isNaN(data[node.testGene.number][exp])) { // convert data value to color Color col = data2Color(node.testGene,data[node.testGene.number][exp]); g.setPaint(col); } else // missing value g.setPaint(Color.white); g.fillRect(x + 2*m, y + h - 4, 2, 1); } g.setPaint(Color.black); // draw vertical split line g.drawLine(x, y, x, y + h); // set font for writing regulator name g.setFont(new Font("SansSerif", Font.BOLD, 4)); FontRenderContext frc = g.getFontRenderContext(); // find dimensions of regulator name LineMetrics metrics = g.getFont().getLineMetrics(node.testGene.name, frc); float regwidth = (float) g.getFont().getStringBounds(node.testGene.name, frc).getWidth(); float regheight = (float) g.getFont().getStringBounds(node.testGene.name, frc).getHeight(); // draw ellipse around regulator name Shape r = new Ellipse2D.Double(x - 0.7 * regwidth, y + h - 11 - 1.4 * regheight + 1.5 * metrics.getDescent(), 1.4 * regwidth, 1.6 * regheight); if (this.TFs.keySet().contains(node.testGene)){ if (this.Genes.contains(node.testGene)){ g.setPaint(Color.orange); } else{ g.setPaint(Color.red); } } else if (this.Genes.contains(node.testGene)){ g.setPaint(Color.yellow); } else{ g.setPaint(Color.white); } g.fill(r); g.setPaint(Color.black); g.draw(r); // write regulator name g.drawString(node.testGene.name, new Float(x - 0.5 * regwidth), new Float(y + h - 11)); // annotate split with its regulator assignment entropy String quality = String.format("(%.2g)", node.entropy); g.setFont(new Font("SansSerif", Font.BOLD, 3)); g.drawString(quality, new Float(x - 2), new Float(y + h + 3)); // x-coordinate for leftChild int xl; if (node.leftChild.nodeStatus.equals("internal")) { // if child is also internal, start should be in the middle of // its own children xl = x - 2*node.leftChild.rightChild.leafDistribution.condSet.size(); } else { // if child is leaf, we draw a vertical to the middle of the // leaf as well as the leaf data point xl = x - 2*node.leftChild.leafDistribution.condSet.size() / 2; g.drawLine(xl, y + h, xl, ybase); int xl1 = x - 2*node.leftChild.leafDistribution.condSet.size(); //draw the condition labels for (int m = 0; m < node.leftChild.leafDistribution.condSet.size(); m++) { int exp = node.leftChild.leafDistribution.condSet.get(m); Condition c = numberedConditions.get(exp); g.setFont(new Font("SansSerif", Font.BOLD, 2)); g.setPaint(Color.black); g.rotate(Math.PI/3,new Float(xl1 + 2*m+1), new Float(ybase + 2*this.Genes.size()+2)); g.drawString(c.name, new Float(xl1 + 2*m+1), new Float(ybase + 2*this.Genes.size()+2)); g.rotate(-Math.PI/3,new Float(xl1 + 2*m+1), new Float(ybase + 2*this.Genes.size()+2)); } // draw the data points int gn = 0; g.setStroke(new BasicStroke(0.25F)); for (Gene gene : this.ordenedGenes) { for (int m = 0; m < node.leftChild.leafDistribution.condSet.size(); m++) { int exp = node.leftChild.leafDistribution.condSet.get(m); if (!Double.isNaN(data[gene.number][exp])) { // convert data to color Color col = data2Color(gene, data[gene.number][exp]); g.setPaint(col); } else // missing value g.setPaint(Color.white); g.fillRect(xl1 + 2*m, ybase + 2*gn, 2, 2); g.setPaint(Color.black); g.drawRect(xl1 + 2*m, ybase + 2*gn, 2, 2); } gn++; } g.setPaint(Color.black); // draw frame around expression values //g.drawRect(xl1, ybase, 2*node.leftChild.leafDistribution.condSet.size(), this.Genes.size()*2); g.setStroke(new BasicStroke(0.5F)); } // x-coordinate for rightChild int xr; if (node.rightChild.nodeStatus.equals("internal")) // if child is also internal, start should be in the middle of // its own children xr = x + 2*node.rightChild.leftChild.leafDistribution.condSet.size(); else { // if child is leaf, we draw a vertical to the middle of the // leaf as well as the leaf data point xr = x + 2*node.rightChild.leafDistribution.condSet.size() / 2; g.drawLine(xr, y + h, xr, ybase); //draw the condition labels for (int m = 0; m < node.rightChild.leafDistribution.condSet.size(); m++) { int exp = node.rightChild.leafDistribution.condSet.get(m); Condition c = numberedConditions.get(exp); g.setFont(new Font("SansSerif", Font.BOLD, 2)); g.setPaint(Color.black); g.rotate(Math.PI/3,new Float(x + 2*m+1), new Float(ybase + 2*this.Genes.size()+2)); g.drawString(c.name, new Float(x + 2*m+1), new Float(ybase + 2*this.Genes.size()+2)); g.rotate(-Math.PI/3,new Float(x + 2*m+1), new Float(ybase + 2*this.Genes.size()+2)); } if(node == this.rightmostNode){ //add labels of non-tree conditions int N = node.rightChild.leafDistribution.condSet.size(); for (int i = 0; i < this.nonTreeConditions.size(); i++) { g.setFont(new Font("SansSerif", Font.BOLD, 2)); g.setPaint(Color.black); g.rotate(Math.PI/3,new Float(x + 2*N +1 + 2*i), new Float(ybase + 2*this.Genes.size()+2)); g.drawString(this.nonTreeConditions.get(i).name, new Float(x + 2*N +1 + 2*i), new Float(ybase + 2*this.Genes.size()+2)); g.rotate(-Math.PI/3,new Float(x + 2*N +1 + 2*i), new Float(ybase + 2*this.Genes.size()+2)); } //add names of overrepresented TFs to plot g.setFont(new Font("SansSerif", Font.BOLD, 2)); g.setPaint(Color.black); int t=0; TreeSet<Gene> ordenedTFs = new TreeSet<Gene>((Set<Gene>) this.TFs.keySet()); for(Gene tf: ordenedTFs){ g.rotate(-Math.PI/2,new Float(x + 2*node.rightChild.leafDistribution.condSet.size() + 2*this.nonTreeConditions.size() +2 + 15 + 2*t), new Float(ybase -2)); g.drawString(tf.name, new Float(x + 2*node.rightChild.leafDistribution.condSet.size() + 2*this.nonTreeConditions.size()+2 + 15 + 2*t), new Float(ybase -2)); g.rotate(Math.PI/2,new Float(x + 2*node.rightChild.leafDistribution.condSet.size() + 2*this.nonTreeConditions.size()+2 + 15 + 2*t), new Float(ybase -2)); t++; } //add names of overrepresented GO cats to plot g.setFont(new Font("SansSerif", Font.BOLD, 2)); g.setPaint(Color.black); t=0; for(OntologyTerm go: GO.keySet()){ g.rotate(-Math.PI/2,new Float(x + 2*node.rightChild.leafDistribution.condSet.size() + 2*this.nonTreeConditions.size()+ 2*ordenedTFs.size() + 4 + 15 + 2*t), new Float(ybase -2)); g.drawString(go.getName(), new Float(x + 2*node.rightChild.leafDistribution.condSet.size() + 2*this.nonTreeConditions.size()+ 2*ordenedTFs.size() +4 + 15 + 2*t), new Float(ybase -2)); g.rotate(Math.PI/2,new Float(x + 2*node.rightChild.leafDistribution.condSet.size() + 2*this.nonTreeConditions.size()+ 2*ordenedTFs.size() +4 + 15 + 2*t), new Float(ybase -2)); t++; } //add names of module links to plot t = 0; g.setFont(new Font("SansSerif", Font.BOLD, 2)); g.setPaint(Color.black); for(Module m: modLinks){ g.rotate(-Math.PI/2,new Float(x + 2*node.rightChild.leafDistribution.condSet.size() + 2*this.nonTreeConditions.size()+ 2*ordenedTFs.size() + 4 + 2*GO.keySet().size() +2 + 15 + 2*t), new Float(ybase -2)); g.drawString(Integer.toString(m.number), new Float(x + 2*node.rightChild.leafDistribution.condSet.size() + 2*this.nonTreeConditions.size()+ 2*ordenedTFs.size() +4 + 2*GO.keySet().size() +2+ 15 + 2*t), new Float(ybase -2)); g.rotate(Math.PI/2,new Float(x + 2*node.rightChild.leafDistribution.condSet.size() + 2*this.nonTreeConditions.size()+ 2*ordenedTFs.size() +4 + 2*GO.keySet().size() +2+ 15 + 2*t), new Float(ybase -2)); t++; } } // draw the data points g.setStroke(new BasicStroke(0.25F)); int gn = 0; for (Gene gene : this.ordenedGenes) { for (int m = 0; m < node.rightChild.leafDistribution.condSet .size(); m++) { int exp = node.rightChild.leafDistribution.condSet.get(m); if (!Double.isNaN(data[gene.number][exp])) { // convert data to color Color col = data2Color(gene, data[gene.number][exp]); g.setPaint(col); } else // missing value g.setPaint(Color.white); g.fillRect(x + 2*m, ybase + 2*gn, 2, 2); g.setPaint(Color.black); g.drawRect(x + 2*m, ybase + 2*gn, 2, 2); } if(node == this.rightmostNode){ int N = node.rightChild.leafDistribution.condSet.size(); //draw non-tree condition data points for (int m = 0; m < this.nonTreeConditions.size(); m++) { int exp = this.nonTreeConditions.get(m).number; if (!Double.isNaN(data[gene.number][exp])) { // convert data to color Color col = data2Color(gene, data[gene.number][exp]); g.setPaint(col); } else // missing value g.setPaint(Color.white); g.fillRect(x + 2*N + 2*m, ybase + 2*gn, 2, 2); g.setPaint(Color.black); g.drawRect(x + 2*N + 2*m, ybase + 2*gn, 2, 2); } // draw line between rightmost leaf and extra conditions if(this.nonTreeConditions.size() > 0){ g.setStroke(new BasicStroke(0.5F)); g.setPaint(Color.white); g.drawLine(x + 2*N, ybase + 2*gn, x + 2*N, ybase + 2*gn + 2); g.setPaint(Color.black); g.setStroke(new BasicStroke(0.25F)); } //add names of genes to plot g.setFont(new Font("SansSerif", Font.BOLD, 2)); g.setPaint(Color.black); g.drawString(gene.name, new Float(x + 2*node.rightChild.leafDistribution.condSet.size() + 2*this.nonTreeConditions.size() +2), new Float(ybase + 2*gn+2)); //add yellow squares for overrepresented TFs int t = 0; TreeSet<Gene> ordenedTFs = new TreeSet<Gene>((Set<Gene>) this.TFs.keySet()); for(Gene tf: ordenedTFs){ if(this.moduleNetwork.getTFBinding().containsKey(tf) && this.moduleNetwork.getTFBinding().get(tf).containsKey(gene)){ g.setPaint(Color.yellow); g.fillRect(x + 2*node.rightChild.leafDistribution.condSet.size()+ 2*this.nonTreeConditions.size() + 15 + 2*t, ybase + 2*gn, 2, 2); } g.setPaint(Color.black); g.drawRect(x + 2*node.rightChild.leafDistribution.condSet.size()+ 2*this.nonTreeConditions.size() + 15 + 2*t, ybase + 2*gn, 2, 2); t++; } //add orange squares for overrepresented GO cats t = 0; for(OntologyTerm go: GO.keySet()){ boolean ok = false; for(OntologyTerm o: gene.GOannotations){ if(o.equals(go)){ ok = true; } } if(ok == true){ g.setPaint(Color.orange); g.fillRect(x + 2*node.rightChild.leafDistribution.condSet.size()+ 2*this.nonTreeConditions.size() + 2*ordenedTFs.size() +2 + 15 + 2*t, ybase + 2*gn, 2, 2); } g.setPaint(Color.black); g.drawRect(x + 2*node.rightChild.leafDistribution.condSet.size()+ 2*this.nonTreeConditions.size() + 2*ordenedTFs.size() +2 + 15 + 2*t, ybase + 2*gn, 2, 2); t++; } //add links to other modules t = 0; for(Module m: modLinks){ if(gene.modules.contains(m)){ g.setPaint(Color.blue); g.fillRect(x + 2*node.rightChild.leafDistribution.condSet.size()+ 2*this.nonTreeConditions.size() + 2*ordenedTFs.size() +2 + 2*GO.keySet().size() +2 + 15 + 2*t, ybase + 2*gn, 2, 2); } g.setPaint(Color.black); g.drawRect(x + 2*node.rightChild.leafDistribution.condSet.size()+ 2*this.nonTreeConditions.size() + 2*ordenedTFs.size() +2 + 2*GO.keySet().size() +2 + 15 + 2*t, ybase + 2*gn, 2, 2); t++; } } gn++; } g.setPaint(Color.black); // draw frame around expression values //g.drawRect(x, ybase, 2*node.rightChild.leafDistribution.condSet.size(), this.Genes.size()*2); g.setStroke(new BasicStroke(0.5F)); } // draw horizontal line between start coordinates for the children g.drawLine(xl, y + h, xr, y + h); // draw the children, right one is drawn lower than left one for clarity drawnode(node.leftChild, xl, y + h, h, ybase, data, g); drawnode(node.rightChild, xr, y + h, h + 4, ybase, data, g); // draw line between leaves g.setPaint(Color.white); g.drawLine(x, ybase, x, ybase + this.Genes.size()*2); g.setPaint(Color.black); } } // draw data as one big leaf (for module without parents) public void draw1leaf(int x, int y, double[][] data, Graphics2D g) { int numCond = this.regressionTree.leafDistribution.condSet.size(); if(numCond != this.Conditions.size()){ System.out.println("Error here"); } int gn = 0; for(int i = 0; i < this.regressionTree.leafDistribution.condSet.size();i++){ Condition c = this.numberedConditions.get(this.regressionTree.leafDistribution.condSet.get(i)); //add names of conditions g.setFont(new Font("SansSerif", Font.BOLD, 2)); g.setPaint(Color.black); g.rotate(Math.PI/3,new Float(x + 2*i+1), new Float(y + 2*this.Genes.size()+2)); g.drawString(c.name, new Float(x + 2*i+1), new Float(y + 2*this.Genes.size()+2)); g.rotate(-Math.PI/3,new Float(x + 2*i+1), new Float(y + 2*this.Genes.size()+2)); } //add names of overrepresented TFs to plot g.setFont(new Font("SansSerif", Font.BOLD, 2)); g.setPaint(Color.black); TreeSet<Gene> ordenedTFs = new TreeSet<Gene>((Set<Gene>) this.TFs.keySet()); int t=0; for(Gene tf: ordenedTFs){ g.rotate(-Math.PI/2,new Float(x + 2*(numCond+1) + 15 + 2*t), new Float(y -2)); g.drawString(tf.name, new Float(x + 2*(numCond+1) + 15 + 2*t), new Float(y -2)); g.rotate(Math.PI/2,new Float(x + 2*(numCond+1) + 15 + 2*t), new Float(y -2)); t++; } //add names of overrepresented GO cats to plot g.setFont(new Font("SansSerif", Font.BOLD, 2)); g.setPaint(Color.black); t=0; for(OntologyTerm go: GO.keySet()){ g.rotate(-Math.PI/2,new Float(x + 2*(numCond+1) + 2*ordenedTFs.size() + 2 + 15 + 2*t), new Float(y -2)); g.drawString(go.getName(), new Float(x + 2*(numCond+1) + 2*ordenedTFs.size() +2 + 15 + 2*t), new Float(y -2)); g.rotate(Math.PI/2,new Float(x + 2*(numCond+1) + 2*ordenedTFs.size() +2 + 15 + 2*t), new Float(y -2)); t++; } //add names of module links to plot t = 0; g.setFont(new Font("SansSerif", Font.BOLD, 2)); g.setPaint(Color.black); for(Module m: modLinks){ g.rotate(-Math.PI/2,new Float(x + 2*(numCond+1) + 2*ordenedTFs.size() + 2 + 2*GO.keySet().size() + 2 + 15 + 2*t), new Float(y -2)); g.drawString(Integer.toString(m.number), new Float(x + 2*(numCond+1) + 2*ordenedTFs.size() +2 + 2*GO.keySet().size() + 2 + 15 + 2*t), new Float(y -2)); g.rotate(Math.PI/2,new Float(x + 2*(numCond+1) + 2*ordenedTFs.size() +2 + 2*GO.keySet().size() + 2 + 15 + 2*t), new Float(y -2)); t++; } g.setStroke(new BasicStroke(0.25F)); for (Gene gene : this.ordenedGenes) { for (int i = 0; i < this.regressionTree.leafDistribution.condSet.size();i++) { int m = this.numberedConditions.get(this.regressionTree.leafDistribution.condSet.get(i)).number; if (!Double.isNaN(data[gene.number][m])) { // convert data to color Color col = data2Color(gene, data[gene.number][m]); g.setPaint(col); } else // missing value g.setPaint(Color.white); g.fillRect(x + 2*i, y + 2*gn, 2, 2); g.setPaint(Color.black); g.drawRect(x + 2*i, y + 2*gn, 2, 2); } //add name of gene g.setFont(new Font("SansSerif", Font.BOLD, 2)); g.setPaint(Color.black); g.drawString(gene.name, new Float(x + 2*(numCond+1)), new Float(y + 2*gn +2)); //add yellow squares for overrepresented TFs t=0; for(Gene tf: ordenedTFs){ if(this.moduleNetwork.getTFBinding().containsKey(tf) && this.moduleNetwork.getTFBinding().get(tf).containsKey(gene)){ g.setPaint(Color.yellow); g.fillRect(x + 2*(numCond) + 15 + 2*t, y + 2*gn, 2, 2); } g.setPaint(Color.black); g.drawRect(x + 2*(numCond) + 15 + 2*t, y + 2*gn, 2, 2); t++; } //add orange squares for overrepresented GO cats t = 0; for(OntologyTerm go: GO.keySet()){ //System.out.println(this.name + "\t" + go.getName()); boolean ok = false; for(OntologyTerm o: gene.GOannotations){ if(o.equals(go)){ //System.out.println(this.name + "\t" + go.getName() + "\t" + o.getName()); ok = true; } } if(ok == true){ g.setPaint(Color.orange); g.fillRect(x + 2*(numCond) + 2*ordenedTFs.size() +2 + 15 + 2*t, y + 2*gn, 2, 2); } g.setPaint(Color.black); g.drawRect(x + 2*(numCond) + 2*ordenedTFs.size() +2 + 15 + 2*t, y + 2*gn, 2, 2); t++; } //add links to other modules t = 0; for(Module m: modLinks){ if(gene.modules.contains(m)){ g.setPaint(Color.blue); g.fillRect(x + 2*(numCond) + 2*ordenedTFs.size() +2 + 2*GO.keySet().size() +2 + 15 + 2*t, y + 2*gn, 2, 2); } g.setPaint(Color.black); g.drawRect(x + 2*(numCond) + 2*ordenedTFs.size() +2 + 2*GO.keySet().size() +2 + 15 + 2*t, y + 2*gn, 2, 2); t++; } gn++; } g.setPaint(Color.black); // draw frame around expression values //g.drawRect(x, y, numCond*2, this.Genes.size()*2); g.setStroke(new BasicStroke(0.5F)); } public void setTFs(HashMap<Gene,Double> tfs){ TFs.putAll(tfs); } }

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[Beg-sysbiol] will you guys and girls be around then?
by Yves Van de Peer 14 Jun '07

14 Jun '07

-------- Original Message -------- Subject: Re: Thanks for the acceptance of my visit on July 20(Fri)-- Toru YAO/RIKEN Date: Thu, 14 Jun 2007 09:20:08 +0900 From: yao <yao(a)riken.jp> To: yao <yao(a)riken.jp> CC: Dirk Inze <dirk.inze(a)psb.UGent.be>, Martin Kuiper <makui(a)psb.UGent.be>, Yves Van de Peer <yves.vandepeer(a)psb.ugent.be>, Hilde Diegenant <hidie(a)psb.UGent.be> References: <02AE15DCD9DADE47925138968C2B9D371F2586(a)hermes.psb.UGent.be> <20070601082057.95A7.YAO(a)riken.jp> Dear Prof.Dirk Inze and Prof.Martin Kuiper; I would like to confirm the time span to visit both of you on July 20 (Fri). I will be free whole day of July 20 by staying at a hotel in Brussell from 18 to 21. I think I will be able to arrive at Ghent around 9:30am of Friday. I don't want to disurbe so much your valuable time, so how about the time span from 10:00am to 12:00am of the day ? (Still I will be free in the afternoon, if you could introduce some persons on animal or microbial systems biology, I would most appreciate.) Looking for hearing from you. With best regards, Toru YAO Advisor, RIKEN On Fri, 01 Jun 2007 09:15:45 +0900 yao <yao(a)riken.jp> wrote: > Dear Prof. Dirk Inze; > > Thank you very much for your quick reply on the acceptance > of my visit in July. > > I will visit you on July 20(Fri). > > Dear Prof. Martin Kuiper; > > As Prof.Inze introduced you, I am very happy to visit you > on July 20(Fri). > > I am very much interested with the Computational Biology, > Bioinformatics and Systems Biology, and would like to hear > your activities and prospects in these fields. > > If possible, please introduce some appropriate persons of > these fields on animals or model organisms. > > I also wanat to visit experimental sites. > > I will be free whole day of July 20, but I don't want to > disturbe so much your valuable time. Please arrange for > separate short time spans. > > I will stay at a hotel in Brussell from 19 to 21. > > Looking forward to hearing from you. > > With best regards, > Toru YAO > > > On Thu, 31 May 2007 12:45:40 +0200 > "Dirk Inze" <dirk.inze(a)psb.UGent.be> wrote: > > > Dear Prof Yao, > > I also enjoyed our brief meeting in RIKEN PSC. You are > > most welcome to visit VIB-Plant Systems Biology on both Thursday 19th > > and Friday 20th July. My senior colleague, Prof Martin Kuiper, head of > > the computational biology group, will be in charge of you visit. Please > > establish direct contacts with Dr Kuiper (makui(a)psb.ugent.be) Both Prof > > Yves Van de Peer (head of the bioinformatics group) and myself are not > > available on Thursday but we will be able to meet and discuss with you > > on Friday. > > I look forward to meet you in July in Ghent. > > > > With kind regards > > Dirk Inze > > ------------------------------------------------------------------------ > > -- > > Prof.Dr.Dirk Inze > > Science Director > > VIB Department of Plant Systems Biology, UGent > > > > Technologiepark 927 > > 9052 Ghent, Belgium > > tel: +32-9-331.38.06 fax: +32-9-331.38.09 > > dirk.inze(a)psb.ugent.be http://www.psb.ugent.be > > ------------------------------------------------------------------------ > > -- > > > > > > > > -----Original Message----- > > From: yao [mailto:yao@riken.jp] > > Sent: donderdag 31 mei 2007 11:46 > > To: diinz(a)psb.UGent.be > > Subject: My visit you in July-- Toru YAO/RIKEN > > > > Dear Prof.Dirk Inze; > > > > It was a good meeting with you at RIKEN here the day before > > yesterday on May 28. > > > > As I said at that time, I would like to visit you at Gent > > either on July 20(Fri) or 19(Thu), if you were acceptable. > > > > I am sorry that my available dates are only above two days. > > I will attend to the ISMB/ECCB in Viena on 21-25 July, and > > leave Japan on July 18 to arrive at Brussell in the evening > > on July 18. > > > > My purpose of this visit is to hear your activities and > > pespectives on the Systems Biology of Plants. > > > > If possible, please introduce the persons on the Systems > > Bilogy of Animals or Model Organisms. > > > > Let me introduce briefly myself. > > I am working as the advisor on Bioinformatics and Systems > > Biology at Genomic Sciences Center of RIKEN for nine years > > from 1998. > > Recently, I am very much interested with the progress of the > > Systems Bilogy in various fields not only for the analyses of > > fundamental biological processes, but also for the applications > > to medical, environmental fields. > > > > I have been talking with Drs.Shinozaki,Saito,Matsui,Deguchi,Seki > > et al on this problem several times. > > > > Anyway, would you please find a short time for me and recommend > > some other appropriate persons ? > > > > Looking forward to hearing from you by return. > > > > With best regards, > > Toru YAO > > yao(a)riken.jp > > 81-45-503-9295 > > RIKEN Yokohama > > > > I will attach my papers and intro. > > > > > > -- > yao <yao(a)postman.riken.go.jp> -- yao <yao(a)postman.riken.go.jp> -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://www.psb.ugent.be/bioinformatics/

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[Beg-sysbiol] LeMoNe
by Yves Van de Peer 09 Jun '07

09 Jun '07

Dear all, Could you please keep me posted on everything that comes out of applying LeMoNe to Arabidopsis data. Thanks in advance, Best regards, Yves -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://www.psb.ugent.be/bioinformatics/

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