Computational approaches to analysis of DNA microarray data.
OBJECTIVE
To review the current state of the art in computational methods for the analysis of DNA microarray data.


METHODS
The review considers methods of microarray data collection, transformation and representation, comparisons and predictions of gene expression from the data, their mechanistic analysis, related systems biology, and the application of clustering techniques.


RESULTS
Functional genomics approaches have greatly increased the rate at which data on biological systems is generated, leading to corresponding challenges in analyzing the data through advanced computational techniques. The paper compares and contrasts the application of computational clustering for discovery, comparison, and prediction of gene expression classes, together with their evaluation and relation to mechanistic analyses of biological systems.


CONCLUSIONS
Methods for assaying gene expression levels by DNA microarray experiments produce considerably more data than other techniques, and require a wide variety of computational techniques for identifying patterns of expression that may be biologically significant. These will have to be verified and validated by comparison to results from other methods, integrated with other systems data, and provide the feedback for further experimentation for testing mechanistic or other biological hypotheses.
Quackenbush
J
J
Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA. johnq@jimmy.harvard.edu
D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D023281:Genomics / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000145:classification / Q000379:methods*