Development and application of a microarray meter tool to optimize microarray experiments

Stochastic Oscillations in Genetic Regulatory Networks: Application to Microarray Experiments

We analyze the stochastic dynamics of genetic regulatory networks using a system of nonlinear differential equations. The system of S-functions is applied to capture the role of RNA polymerase in the transcription-translation mechanism. Using probabilistic properties of chemical rate equations, we derive a system of stochastic differential equations which are analytically tractable despite the ...

Development of a new reference standard for microarray experiments.

Often microarray studies require a reference to indirectly compare the samples under observation. References based on pooled RNA from different cell lines have already been described (here referred to as RNA-R), but they usually do not exhaustively represent the set of genes printed on a chip, thus requiring many adjustments during the analyses. A reference could also be generated in vitro tran...

cDNA Microarray Data Normalization

Functional interpretation of microarray experiments.

Over the past few years, due to the popularisation of high-throughput methodologies such as DNA microarrays, the possibility of obtaining experimental data has increased significantly. Nevertheless, the interpretation of the results, which involves translating these data into useful biological knowledge, still remains a challenge. The methods and strategies used for this interpretation are in c...

Multiplicity issues in microarray experiments.

OBJECTIVES Discussion of different error concepts relevant to microarray experiments. Review of some commonly used multiple testing procedures. Comparison of different approaches as applied to gene expression data. METHODS This article focuses on familywise error rate (FWER) and false discovery rate (FDR) controlling procedures. Methods under investigation include: Bonferroni-type methods and...