Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis.
BACKGROUND
Microarray technology provides access to expression levels of thousands of genes at once, producing large amounts of data. These datasets are valuable only if they are annotated by sufficiently detailed experiment descriptions. However, in many databases a substantial number of these annotations is in free-text format and not readily accessible to computer-aided analysis.


RESULTS
The Multi-Conditional Hybridization Intensity Processing System (M-CHIPS), a data warehousing concept, focuses on providing both structure and algorithms suitable for statistical analysis of a microarray database's entire contents including the experiment annotations. It addresses the rapid growth of the amount of hybridization data, more detailed experimental descriptions, and new kinds of experiments in the future. We have developed a storage concept, a particular instance of which is an organism-specific database. Although these databases may contain different ontologies of experiment annotations, they share the same structure and therefore can be accessed by the very same statistical algorithms. Experiment ontologies have not yet reached their final shape, and standards are reduced to minimal conventions that do not yet warrant extensive description. An ontology-independent structure enables updates of annotation hierarchies during normal database operation without altering the structure.


BACKGROUND
http://www.dkfz.de/tbi/services/mchips
Fellenberg
Kurt
K
Department of Theoretical Bioinformatics, German Cancer Research Center, PO Box 101949, D-69009 Heidelberg, Germany. k.fellenberg@dkfz.de
Hauser
Nicole C
NC
Brors
Benedikt
B
Hoheisel
Jörg D
JD
Vingron
Martin
M
D000465:Algorithms; D003627:Data Interpretation, Statistical; D003628:Database Management Systems; D016208:Databases, Factual; D030541:Databases, Genetic; D015870:Gene Expression; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011786:Quality Control; D012985:Software Design