Inhalt

•  
   List of Figures
•  
   List of Tables
•  
   Motivation and Overview
•  
   Introduction
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   Information Flow and Regulation in the Cell
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   The New 'Omics Approaches
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   Analysis of Transcriptional Regulation -- Goals and Visions
•  
   Open Source Software in 'Omics Research
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  Analysis of Gene-Expression
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   Microarray Technology
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   Spotted Two-Color Microarrays
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   In-Situ Synthesized Microarrays
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   Applications of Microarrays for Genomic DNA Hybridizations
•  
   Tiling Arrays
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   Protein Arrays
•  
   A Sample Analysis Pipeline
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  Properties Of Microarray Data
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   Variation and Replication
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   Preprocessing and Normalization
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  Inferring Significant Changes
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   Statistical tests
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   Student's T-Test
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   Wilcoxon's Rank-Sum Test
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   Bayesian Testing -- CyberT
•  
   Linear Models and Empirical Bayes Methods -- LIMMA
•  
   Permutation Testing -- SAM
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   Rank Products
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   The VarMixt Approach
•  
   Tests for More than Two Groups
•  
   Multiple Testing
•  
  Machine Learning Approaches
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   Cluster Analysis
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   Supervised Machine Learning
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   Towards Systems Biology
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  State of the Art in Systems and Standards
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   Standardization and Specification
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   MIAME
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   MAGE
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   Ontologies
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   Other Standardization Approaches
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   Categorization of Microarray Software
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   Scanner and Image Analysis Software
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  Pure Data Analysis Software
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    Eisen's Cluster and TreeView
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   J-Express
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   Public Repositories and Databases
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   ArrayExpress
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   Stanford Microarray Database
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   CIBEX
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   NCBI GEO
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   LIMS Software
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  General Purpose Analysis and Storage Systems
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   TIGR TM4
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   BASE
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   MARS
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   Rosetta Biosoftware Resolver
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  Extensions to Existing Programming Environments
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   Bioconductor and R
•  
  Requirements and Specification
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   Use Cases
•  
   User Interface
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  Technical Requirements and Preconditions
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   Data Handling
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   Data Analysis Capabilities
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   Data Integration
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   Existing Systems Revisited
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  Object-Oriented System Design
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   Architecture
•  
   Object Model
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   MAGE-OM Classes as Core Persistence Model
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   Access Control Model
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   Data-Analysis Model for PlugIns
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  Implementation
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  Choice of Core Development Tools
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   Database Backend
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   Programming Languages and Tools
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   Object-Relational Mapping With O2DBI
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   Mapping of MAGE-OM Classes on O2DBI Classes using XML Transformations
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  Web-Interface
•  
   The Web-Interface
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   The ArrayLIMS Interface
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   Access Control
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   Ontology Integration
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  Data Integration and Interoperability
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   BRIDGE
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   Web-Services and BioMoby
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   EMMA2 as a Web-Service Provider
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   EMMA2 as a Web-Service Client
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  Implementation of Data Analysis
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   Function Definition
•  
   The Pipeline API
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   Normalization and Preprocessing
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   Statistical Tests
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   Cluster-Analysis
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   Visualization Methods
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   Scatterplots and MA-plots
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   KEGG-Mapping
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   Categorial PCA-plots
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   Cluster Visualization
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   3D-SOM Viewer
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  Applications and their Results
•  
   Overview of the Various EMMA2 Projects
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   The GenoMik Microarray Database
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   Project Specific Requirements and Results
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   Evaluation of Statistical Tests
•  
   Materials and Methods
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   Results
•  
   Stress Response Analysis of S. meliloti
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   Project Setup
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   Experiment Design
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   Management of Experimental Protocols and Data
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   Identification of Significant Functional Categories
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   The Plant Microarray Databases
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   Project Specific Requirements
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   Project Setup
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   Results
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  The Mamma Carcinoma Microarray Database
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   Project Specific Requirements and Results
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   Discussion