ncbb2010

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CSB.DB - A Comprehensive System-Biology Database - Hosted at Max Planck Institute of Molecular Plant Physiology Bjoern Usadel Dirk Steinhauser CSB.DB – Development Core Team Research groups: Plant Cell Walls (M. Pauly) & Root Metabolism (J.Kopka) URL: http://csbdb.mpimp-golm.mpg.de/ Introduction Max Planck Institute of Molecular Plant Physiology Steinhauser, D., Usadel, B., Luedemann, A., Thimm, O. & Kopka, J. (2004a) Bioinformatics, accepted

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Oltvai, Z.N. & Barabási, A.-L. Life`s Complexity Pyramide. Sciene 298, 763-764 (2002) Life`s Complexity Pyramide new easily accessible knowledge about the relationship / hierarchy of cellular components understanding life’s complexity pyramid formulation of hypotheses about the respective functional involvement of compounds / their (inter-) relationships Goals: Bioinformatics Biophysics Biochemistry Bioengineering & Bionics CSB.DB Biostatistics Ecology Evolution Molecular Biology & Physiology Biology The multidisciplinary crosstalk Max Planck Institute of Molecular Plant Physiology CSB Project

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Association among entities: Genes, Proteins, Enzyme activities, Metabolites  co-regulated entities Max Planck Institute of Molecular Plant Physiology Co-Response measure: Correlation, Distances, Mutual Information Functional prediction of sets of non-homologous genes Identification of genes which embody a specific functional category: marker genes Evolution & gene (co-response) Similarity measures Distance measures Pearson KendallSpearman ... Euclidean Manhattan ... Co-Response Analyses

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Max Planck Institute of Molecular Plant Physiology - publicly available - well measurements - manual assignments Genes Genes Genes EXPT - NA omit (5%) - subsets - conditional - global Software-Development@CSB.DB cCoRv1.0: - non- / semi- / parametric - distance / similarity - incl. statistics (pval, power,CI) - large data sets EXPT CSB.DB: Profile Processing

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Max Planck Institute of Molecular Plant Physiology cCoR CoRDB Server Txt R Perl CGI Client WWW Java Applet Interactive Applet CGI Call SAP DB HTML Tmp R statistical package Database Text Files Programs Tmp Folder: gif‘s CGI-Script Modules CoRDB Server Web Server PM PM SuSE Linux Server Site Client Site public web interface  large scale stat. analyses became operational in March 2004 CSB.DB: System Architecture

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Max Planck Institute of Molecular Plant Physiology Genome RNA Proteins Metabolites Information Storage Processing Execution Higher order organisation Universality Organism specificity Analytic Co-Response Databases Metabolic & Analytical Databases CSB.DB Associated Web Pages genes metabolites CSB.DB Structure: current & future

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Max Planck Institute of Molecular Plant Physiology Query Types - Single (Gene) Query - Multiple (Gene) Query - Intersection (Gene) Query Info / Help Default Settings Query Group - Easy - Advanced CSB.DB CoR.DBs Functions

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multiple gene query single / intersection gene query MapMan Visualisation: (Thimm et al., 2004) CoRNetApplet: Tables (HTML) Functional Category Summary Max Planck Institute of Molecular Plant Physiology CSB.DB: Co-Response Query Thimm et al. (2004) Plant J., 37, 914-939

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CSB.DB Max Planck Institute of Molecular Plant Physiology CSB.DB Validation / Graphs

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CSB.DB Proof of Concept Max Planck Institute of Molecular Plant Physiology Steinhauser, D., Junker, B.H., Luedemann, A., Selbig, J. & Kopka, J. (2004b) Bioinformatics, DOI: 10.1093/bioinformatics/bth182. E. coli  Operon Prediction: Scheme: Hypotheses driven approach (HDA) Results: Unbiased cluster approach failed Integration of additional information, i.e. chromosomal distance, increase precision of annotation Distribution of robust correlation among Operon genes & Non-operon genes

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Outlook Max Planck Institute of Molecular Plant Physiology Context dependent Metabolic pathways Thimm et al. (2004) Plant J., 37, 914-939 Luedemann et al. (2004) Bioinformatics Advance Access published on April 22 MapMan Visualisation: (Thimm et al., 2004) PaVESy Visualisation: (Luedemann et al., 2004)

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Acknowledgements Max Planck Institute of Molecular Plant Physiology Contributors of CSB.DB Alexander Luedemann: CoRNetApplet Leonard Krall & Dirk Buessis: Improvements & Discussions Joachim Kopka: MSRI@CSB.DB Claudia Birkemeyer: Analytics@CSB.DB Oliver Thimm & Yves Gibon: MapMan Charles Guy & Co-Workers: Unpublished Experiments J. Selbig: Escherichia coli & Discussions Support of CSB.DB Joachim Kopka, Thomas Altmann, Lothar Willmitzer, Mark Stitt Biological Projects & Cooperation S. Kempa, C. Rautengarten & T. Altmann, J. Lisso & C. Müssig, W.R. Scheible, M. Udvardi, A. Niehl, F. Carrari, V. Nikiforova Server & Admin: E. Simmat & P. Krueger:  Server administration & Discussions