PowerPoint-Pr

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Introduction
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/
Max Planck Institute of Molecular Plant Physiology
Steinhauser, D., Usadel, B., Luedemann, A.,
Thimm, O. Kopka, J. (2004a) Bioinformatics,
accepted
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CSB Project
Goals

• new easily accessible knowledge about the
  relationship / hierarchy of cellular components
• understanding lifes complexity pyramid
• formulation of hypotheses about the respective
  functional involvement of compounds / their
  (inter-) relationships

Lifes Complexity Pyramide
The multidisciplinary crosstalk
Bioinformatics
Bioengineering Bionics
Biostatistics
CSB.DB
Ecology
Biophysics
Biology
Evolution
Molecular Biology Physiology
Biochemistry
Max Planck Institute of Molecular Plant Physiology
Oltvai, Z.N. Barabási, A.-L. Lifes Complexity
Pyramide. Sciene 298, 763-764 (2002)
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Co-Response Analyses

• Association among entities Genes, Proteins,
  Enzyme activities, Metabolites ?
  co-regulated entities

• Functional prediction of sets of non-homologous
  genes
• Identification of genes which embody a specific
  functional category marker genes
• Evolution gene (co-response)

• Co-Response measure Correlation, Distances,
  Mutual Information

Similarity measures
Pearson KendallSpearman ...
Distance measures
Euclidean Manhattan ...
Max Planck Institute of Molecular Plant Physiology
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CSB.DB Profile Processing
EXPT
Genes
- publicly available - well measurements - manual
assignments
EXPT
- NA omit (5) - subsets - conditional - global
Genes
Genes
Software-Development_at_CSB.DB
- non- / semi- / parametric - distance /
similarity - incl. statistics (pval, power,CI) -
large data sets
cCoRv1.0
Max Planck Institute of Molecular Plant Physiology
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CSB.DB System Architecture

• public web interface ? large scale stat. analyses
• became operational in March 2004

Database
SAP DB
R statistical package
R
PM
Client Site
CoRDB Server
CGI Call
Perl CGI
Txt
WWW
Client
Text Files
HTML
cCoR
Java Applet
PM
Tmp
Programs
Interactive Applet
Tmp Folder gifs
CGI-Script Modules
CoRDB Server
Web Server
SuSE Linux
Server Site
Max Planck Institute of Molecular Plant Physiology
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CSB.DB Structure current future
Higher order organisation
Universality
Organism specificity
Genome
CSB.DB Associated Web Pages
Information Storage
genes
RNA
Processing
Proteins
Co-Response Databases
Analytic
Execution
metabolites
Metabolic Analytical Databases
Metabolites
Max Planck Institute of Molecular Plant Physiology
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CSB.DB CoR.DBs Functions
Query Types
- Single (Gene) Query - Multiple (Gene) Query -
Intersection (Gene) Query
Query Group
- Easy - Advanced
Info / Help
Default Settings
Max Planck Institute of Molecular Plant Physiology
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CSB.DB Co-Response Query
MapMan Visualisation (Thimm et al., 2004)
single / intersection gene query
Functional Category Summary
Tables (HTML)
multiple gene query
CoRNetApplet
Max Planck Institute of Molecular Plant Physiology
Thimm et al. (2004) Plant J., 37, 914-939
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CSB.DB Validation / Graphs
CSB.DB
Max Planck Institute of Molecular Plant Physiology
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CSB.DB Proof of Concept
E. coli ? Operon Prediction
Distribution of robust correlation among Operon
genes Non-operon genes
Scheme Hypotheses driven approach (HDA)

• Results
• Unbiased cluster approach failed
• Integration of additional information, i.e.
  chromosomal distance, increase precision of
  annotation

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.
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Outlook
MapMan Visualisation (Thimm et al., 2004)
Context dependent
Metabolic pathways
PaVESy Visualisation (Luedemann et al., 2004)
Max Planck Institute of Molecular Plant Physiology
Luedemann et al. (2004) Bioinformatics Advance
Access published on April 22
Thimm et al. (2004) Plant J., 37, 914-939
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Acknowledgements
Contributors of CSB.DB Alexander Luedemann
CoRNetApplet Leonard Krall Dirk Buessis
Improvements Discussions Joachim Kopka
MSRI_at_CSB.DB Claudia Birkemeyer
Analytics_at_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
Max Planck Institute of Molecular Plant Physiology