Computational Methods and Bioinformatic Tools

Chapter 7 Computational Methods and Bioinformatic Tools Dr. Paul Cullen, Ogham GmbH, Mendelstr. 11, 48149 Münster, GermanySearch for more papers by this authorDr. Stefan Lorkowski, Institute of Arteriosclerosis Research, University of Münster, Domagkstr. 3, 48149 Münster, GermanySearch for more papers by this authorSteffen Hennig, Max Planck Institut für Molekulare Genetik, Berlin (Germany)Search for more papers by this authorAlbert Poustka, Max Planck Institut für Molekulare Genetik, Berlin (Germany)Search for more papers by this authorGeorgia Panopoulou, Max Planck Institut für Molekulare Genetik, Berlin (Germany)Search for more papers by this authorHans Lehrach, Max Planck Institut für Molekulare Genetik, Berlin (Germany)Search for more papers by this authorEberhard Korsching, University of Münster, Münster (Germany)Search for more papers by this authorOxana Pickeral, Human Genome Sciences, Inc., Rockville (USA)Search for more papers by this authorRalf Herwig, Max Planck Institut für Molekulare Genetik, Berlin (Germany)Search for more papers by this authorAlexander Kel, BIOBASE GmbH, Wolfenbüttel (Germany)Search for more papers by this authorDmitrij Tchekmenev, BIOBASE GmbH, Wolfenbüttel (Germany)Search for more papers by this authorEdgar Wingender, BIOBASE GmbH, Wolfenbüttel (Germany)Search for more papers by this authorJohannes Streicher, University of Vienna, Vienna (Austria)Search for more papers by this authorGerd B. Müller, University of Vienna, Vienna (Austria)Search for more papers by this authorTakeshi Kawashima, Kyoto University, Kyoto (Japan)Search for more papers by this authorKazuhiro W. Makabe, Kyoto University, Kyoto (Japan)Search for more papers by this authorInna Dubchak, Lawrence Berkeley National Laboratory, Berkeley (USA)Search for more papers by this authorHongkai Ji, Tsinghua University, Beijing (People's Republic of China)Search for more papers by this authorKousaku Okubo, Kyushu University, Fukuoka (Japan)Search for more papers by this authorShoko Kawamoto, Medical Institute for Bioregulation, Fukuoka (Japan)Search for more papers by this authorEllen Fricke, BIOBASE GmbH, Wolfenbüttel (Germany)Search for more papers by this authorDagmar Karas, BIOBASE GmbH, Wolfenbüttel (Germany)Search for more papers by this authorMartin Haubrock, BIOBASE GmbH, Wolfenbüttel (Germany)Search for more papers by this authorSigrid Land, BIOBASE GmbH, Wolfenbüttel (Germany)Search for more papers by this authorStella Rotert, BIOBASE GmbH, Wolfenbüttel (Germany)Search for more papers by this authorXin Chen, The National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing (People's Republic of China)Search for more papers by this authorJoan Pontius, National Center for Biotechnology Information, National Institute of Health, Bethesda (USA)Search for more papers by this authorEric Eveno, Genexpress, Centre National de la Recherche Scientifique, Villejuif Cedex (France)Search for more papers by this authorCharles Auffray, Genexpress, Centre National de la Recherche Scientifique, Villejuif Cedex (France)Search for more papers by this authorCharles Decraene, Commisariat á l'Ènergie Atomique (CEA), Evry Cedex (France)Search for more papers by this authorClaude Chelala, Genexpress, Centre National de la Recherche Scientifique, Villejuif Cedex (France)Search for more papers by this authorGeneviève Piétu, Commisariat á l'Ènergie Atomique (CEA), Evry Cedex (France)Search for more papers by this authorMarie-Dominique Devignes, LORIA – Langue et dialogue, Vandoeuvre les Nancy (France)Search for more papers by this authorRégine Mariage-Samson, Genexpress, Centre National de la Recherche Scientifique, Villejuif Cedex (France)Search for more papers by this authorSandrine Imbeaud, Genexpress, Centre National de la Recherche Scientifique, Villejuif Cedex (France)Search for more papers by this authorSylvie Bortoli, Commisariat á l'Ènergie Atomique (CEA), Evry Cedex (France)Search for more papers by this authorAlon Amit, Compugen Ltd., Jamesburg (USA)Search for more papers by this authorMartin Ringwald, The Jackson Laboratory, Bar Harbor (USA)Search for more papers by this authorMichael J. de Veer, The Walter and Eliza Hall Institute of Medical Research, The Royal Melbourne Hospital, Victoria (Australia)Search for more papers by this authorBryan R. G. Williams, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland (USA)Search for more papers by this authorEldon M. Walker, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland (USA)Search for more papers by this authorJamie A. Davies, University of Edinburgh, Medical School, Edinburgh (UK)Search for more papers by this authorChristoph Grunau, Institute de Génétique Humain, Montpellier (France)Search for more papers by this authorRichard Baldock, Western General Hospital, Edinburgh (UK)Search for more papers by this authorDuncan R. Davidson, Western General Hospital, Edinburgh (UK)Search for more papers by this authorChristian J. Stoeckert Jr., University of Pennsylvania, Philadelphia (USA)Search for more papers by this authorAngel Pizarro, University of Pennsylvania, Philadelphia (USA)Search for more papers by this authorElisabetta Manduchi, University of Pennsylvania, Philadelphia (USA)Search for more papers by this authorGregory R. Grant, University of Pennsylvania, Philadelphia (USA)Search for more papers by this authorJonathan Crabtree, Center for Bioinformatics, University of Pennsylvania, Philadelphia (USA)Search for more papers by this authorJunmin Liu, University of Pennsylvania, Philadelphia (USA)Search for more papers by this authorPhuc V. Le, University of Pennsylvania, Philadelphia (USA)Search for more papers by this authorShannon K. McWeeney, University of Pennsylvania, Philadelphia (USA)Search for more papers by this authorStephen Welle, University of Rochester, Rochester (USA)Search for more papers by this authorCatherine A. Ball, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorDavid Botstein, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorGail Binkley, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorGavin J. Sherlock, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorJ. Michael Cherry, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorKara Dolinski, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorLaurie Issel-Tarver, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorMark Schroeder, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorSelina S. Dwight, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorShuai Wenig, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorJohn C. Matese, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorHeng Jin, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorJeremy Gollub, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorJoan Hebert, Center for Clinical Sciences Research, Stanford (USA)Search for more papers by this authorMiroslava Kaloper, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorPatrick O. Brown, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorTina Hernandez-Boussard, Center for Clinical Sciences Research, Stanford (USA)Search for more papers by this authorAnuj Kumar, Cellular and Developmental Biology, Yale University, New Haven (USA)Search for more papers by this authorKei-Hoi Cheung, School of Medicine, Yale University, New Haven (USA)Search for more papers by this authorLuis Marenco, School of Medicine, Yale University, New Haven (USA)Search for more papers by this authorMichael Snyder, School of Medicine, Yale University, New Haven (USA)Search for more papers by this authorNick Tosches, School of Medicine, Yale University, New Haven (USA)Search for more papers by this authorPaul Bertone, School of Medicine, Yale University, New Haven (USA)Search for more papers by this authorPerry Miller, School of Medicine, Yale University, New Haven (USA)Search for more papers by this authorPeter Masiar, School of Medicine, Yale University, New Haven (USA)Search for more papers by this authorYang Liu, School of Medicine, Yale University, New Haven (USA)Search for more papers by this authorGraziano Pesole, University of Milan, Milan (Italy)Search for more papers by this authorPhilippe Marc, Ecole Normale Supérieure, Paris (France)Search for more papers by this authorMargaret Biswas, ViaLactia Biosciences Ltd., Auckland (New Zealand)Search for more papers by this authorPaul Kersey, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton (UK)Search for more papers by this authorRolf Apweiler, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton (UK)Search for more papers by this authorChristine Hoogland, Swiss Institute of Bioinformatics, Geneva (Switzerland)Search for more papers by this author Dr. Paul Cullen, Ogham GmbH, Mendelstr. 11, 48149 Münster, GermanySearch for more papers by this authorDr. Stefan Lorkowski, Institute of Arteriosclerosis Research, University of Münster, Domagkstr. 3, 48149 Münster, GermanySearch for more papers by this authorSteffen Hennig, Max Planck Institut für Molekulare Genetik, Berlin (Germany)Search for more papers by this authorAlbert Poustka, Max Planck Institut für Molekulare Genetik, Berlin (Germany)Search for more papers by this authorGeorgia Panopoulou, Max Planck Institut für Molekulare Genetik, Berlin (Germany)Search for more papers by this authorHans Lehrach, Max Planck Institut für Molekulare Genetik, Berlin (Germany)Search for more papers by this authorEberhard Korsching, University of Münster, Münster (Germany)Search for more papers by this authorOxana Pickeral, Human Genome Sciences, Inc., Rockville (USA)Search for more papers by this authorRalf Herwig, Max Planck Institut für Molekulare Genetik, Berlin (Germany)Search for more papers by this authorAlexander Kel, BIOBASE GmbH, Wolfenbüttel (Germany)Search for more papers by this authorDmitrij Tchekmenev, BIOBASE GmbH, Wolfenbüttel (Germany)Search for more papers by this authorEdgar Wingender, BIOBASE GmbH, Wolfenbüttel (Germany)Search for more papers by this authorJohannes Streicher, University of Vienna, Vienna (Austria)Search for more papers by this authorGerd B. Müller, University of Vienna, Vienna (Austria)Search for more papers by this authorTakeshi Kawashima, Kyoto University, Kyoto (Japan)Search for more papers by this authorKazuhiro W. Makabe, Kyoto University, Kyoto (Japan)Search for more papers by this authorInna Dubchak, Lawrence Berkeley National Laboratory, Berkeley (USA)Search for more papers by this authorHongkai Ji, Tsinghua University, Beijing (People's Republic of China)Search for more papers by this authorKousaku Okubo, Kyushu University, Fukuoka (Japan)Search for more papers by this authorShoko Kawamoto, Medical Institute for Bioregulation, Fukuoka (Japan)Search for more papers by this authorEllen Fricke, BIOBASE GmbH, Wolfenbüttel (Germany)Search for more papers by this authorDagmar Karas, BIOBASE GmbH, Wolfenbüttel (Germany)Search for more papers by this authorMartin Haubrock, BIOBASE GmbH, Wolfenbüttel (Germany)Search for more papers by this authorSigrid Land, BIOBASE GmbH, Wolfenbüttel (Germany)Search for more papers by this authorStella Rotert, BIOBASE GmbH, Wolfenbüttel (Germany)Search for more papers by this authorXin Chen, The National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing (People's Republic of China)Search for more papers by this authorJoan Pontius, National Center for Biotechnology Information, National Institute of Health, Bethesda (USA)Search for more papers by this authorEric Eveno, Genexpress, Centre National de la Recherche Scientifique, Villejuif Cedex (France)Search for more papers by this authorCharles Auffray, Genexpress, Centre National de la Recherche Scientifique, Villejuif Cedex (France)Search for more papers by this authorCharles Decraene, Commisariat á l'Ènergie Atomique (CEA), Evry Cedex (France)Search for more papers by this authorClaude Chelala, Genexpress, Centre National de la Recherche Scientifique, Villejuif Cedex (France)Search for more papers by this authorGeneviève Piétu, Commisariat á l'Ènergie Atomique (CEA), Evry Cedex (France)Search for more papers by this authorMarie-Dominique Devignes, LORIA – Langue et dialogue, Vandoeuvre les Nancy (France)Search for more papers by this authorRégine Mariage-Samson, Genexpress, Centre National de la Recherche Scientifique, Villejuif Cedex (France)Search for more papers by this authorSandrine Imbeaud, Genexpress, Centre National de la Recherche Scientifique, Villejuif Cedex (France)Search for more papers by this authorSylvie Bortoli, Commisariat á l'Ènergie Atomique (CEA), Evry Cedex (France)Search for more papers by this authorAlon Amit, Compugen Ltd., Jamesburg (USA)Search for more papers by this authorMartin Ringwald, The Jackson Laboratory, Bar Harbor (USA)Search for more papers by this authorMichael J. de Veer, The Walter and Eliza Hall Institute of Medical Research, The Royal Melbourne Hospital, Victoria (Australia)Search for more papers by this authorBryan R. G. Williams, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland (USA)Search for more papers by this authorEldon M. Walker, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland (USA)Search for more papers by this authorJamie A. Davies, University of Edinburgh, Medical School, Edinburgh (UK)Search for more papers by this authorChristoph Grunau, Institute de Génétique Humain, Montpellier (France)Search for more papers by this authorRichard Baldock, Western General Hospital, Edinburgh (UK)Search for more papers by this authorDuncan R. Davidson, Western General Hospital, Edinburgh (UK)Search for more papers by this authorChristian J. Stoeckert Jr., University of Pennsylvania, Philadelphia (USA)Search for more papers by this authorAngel Pizarro, University of Pennsylvania, Philadelphia (USA)Search for more papers by this authorElisabetta Manduchi, University of Pennsylvania, Philadelphia (USA)Search for more papers by this authorGregory R. Grant, University of Pennsylvania, Philadelphia (USA)Search for more papers by this authorJonathan Crabtree, Center for Bioinformatics, University of Pennsylvania, Philadelphia (USA)Search for more papers by this authorJunmin Liu, University of Pennsylvania, Philadelphia (USA)Search for more papers by this authorPhuc V. Le, University of Pennsylvania, Philadelphia (USA)Search for more papers by this authorShannon K. McWeeney, University of Pennsylvania, Philadelphia (USA)Search for more papers by this authorStephen Welle, University of Rochester, Rochester (USA)Search for more papers by this authorCatherine A. Ball, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorDavid Botstein, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorGail Binkley, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorGavin J. Sherlock, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorJ. Michael Cherry, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorKara Dolinski, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorLaurie Issel-Tarver, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorMark Schroeder, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorSelina S. Dwight, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorShuai Wenig, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorJohn C. Matese, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorHeng Jin, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorJeremy Gollub, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorJoan Hebert, Center for Clinical Sciences Research, Stanford (USA)Search for more papers by this authorMiroslava Kaloper, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorPatrick O. Brown, School of Medicine, Stanford University, Stanford (USA)Search for more papers by this authorTina Hernandez-Boussard, Center for Clinical Sciences Research, Stanford (USA)Search for more papers by this authorAnuj Kumar, Cellular and Developmental Biology, Yale University, New Haven (USA)Search for more papers by this authorKei-Hoi Cheung, School of Medicine, Yale University, New Haven (USA)Search for more papers by this authorLuis Marenco, School of Medicine, Yale University, New Haven (USA)Search for more papers by this authorMichael Snyder, School of Medicine, Yale University, New Haven (USA)Search for more papers by this authorNick Tosches, School of Medicine, Yale University, New Haven (USA)Search for more papers by this authorPaul Bertone, School of Medicine, Yale University, New Haven (USA)Search for more papers by this authorPerry Miller, School of Medicine, Yale University, New Haven (USA)Search for more papers by this authorPeter Masiar, School of Medicine, Yale University, New Haven (USA)Search for more papers by this authorYang Liu, School of Medicine, Yale University, New Haven (USA)Search for more papers by this authorGraziano Pesole, University of Milan, Milan (Italy)Search for more papers by this authorPhilippe Marc, Ecole Normale Supérieure, Paris (France)Search for more papers by this authorMargaret Biswas, ViaLactia Biosciences Ltd., Auckland (New Zealand)Search for more papers by this authorPaul Kersey, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton (UK)Search for more papers by this authorRolf Apweiler, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton (UK)Search for more papers by this authorChristine Hoogland, Swiss Institute of Bioinformatics, Geneva (Switzerland)Search for more papers by this author Book Editor(s):Dr. Stefan Lorkowski, Institute of Arteriosclerosis Research, University of Münster, Domagkstr. 3, 48149 Münster, GermanySearch for more papers by this authorDr. Paul Cullen, Ogham GmbH, Mendelstr. 11, 48149 Münster, GermanySearch for more papers by this author First published: 01 December 2002 https://doi.org/10.1002/352760149X.ch7 AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinked InRedditWechat Summary This chapter contains sections titled: Introduction Comparative expressed sequence tag analysis Introduction Processing expressed sequence tags prior to content analysis Gene content and annotation of expressed sequence tags Expressed sequence tags in comparative genomics In silico subtraction using clustered sets of expressed sequence tags Expressed sequence tag data repositories and cDNA clone distribution centres Data management and data mining Introduction Current situation Future development Taking part in bioinformatics Hardware and software demands Data types, structures and processing Communication structures Building a test scenario Microarray experiments Analysing the workflow – getting things done Designing the question and choosing the right tools for the answer Scaling up Strategies of data mining Data evaluation and representation Principles of query languages Data mining Custom solutions Summary Integration of heterogeneous high-throughput gene expression data Introduction Steps towards data integration Initial steps in realising data integration Conclusions Cluster analysis of gene expression profiles Introduction Information content of gene expression clusters Similarity matrices and gene expression matrices Clustering algorithms Hierarchical clustering Self-organising maps K-means Gene shaving Evaluation of gene expression clusters Conclusion Promoter finding in eukaryotic genomes Introduction Transcription regulation in eukaryotes Promoter structure Transcription factors Combinatorial nature of transcription regulation Databases on transcriptional regulation In silico study of gene transcription regulation Recognition of cis-regulatory elements Recognition of composite regulatory elements Recognition of promoters Conclusions GeneEMAC – Three-dimensional visualisation of gene expression Introduction Principles and basics of the GeneEMAC concept Specimen preparation Whole-mount in situ hybridisation Embedding Introduction of external markers Capturing of a reference image Histological sectioning Microscopy and digital image processing Image capturing Image congruencing Image segmentation Generation of a three-dimensional model Visualisations of models Examples Discussion RNA-based gene expression databases and analyses tools Introduction ASDB – The Alternative Splicing Database AsMamDB – The Alternative Splice Database of Mammals BodyMap – An anatomical gene expression database of human and mouse The CYTOMER® Gene Expression Database on human organs and cell types Database of three-dimensional visualisation of gene expression dbEST – The Database of Expressed Sequence Tags DDD – Digital Differential Display The Genexpress IMAGE Knowledge Base of the Human Genome and Transcriptomes The GencartaTM Database GEO – Gene Expression Omnibus Database GXD – The Mouse Gene Expression Database ISG Database – Interferon-Stimulated Gene Database The Kidney Development Database MAGEST – The Maboya Gene Expression Patterns and Sequence Tags Database MethDB – The DNA Methylation Database EMAGE – The Edinburgh Mouse Atlas Gene Expression Database RAD – The RNA Abundance Database The Rochester Muscle Database SAGEmap – The serial analysis of gene expression tag to gene mapping database SGD – The Saccharomyces Genome Database and its Expression Connection SMD – The Stanford Microarray Database TRIPLES – The Database of Transposon-Insertion Phenotypes, Localisation, and Expression in Saccharomyces cerevisiae UTRdb and UTRsite – The Specialised Databases of Sequences and Functional Elements of 5′ and 3′-Untranslated Regions of Eukaryotic mRNAs yMGV – The Yeast Microarray Global Viewer Protein-based gene expression databases and analyses tools Introduction to protein-based gene expression databases The Proteome Analysis Database SWISS-2DPAGE – A two-dimensional polyacrylamide gel electrophoresis database Further gene-expression databases in the internet Summary References Analysing Gene Expression: A Handbook of Methods: Possibilities and Pitfalls RelatedInformation