Robust test method for time-course microarray experiments.

TitleRobust test method for time-course microarray experiments.
Publication TypeJournal Article
Year of Publication2010
AuthorsSohn, Insuk, Kouros Owzar, Stephen L. George, Sujong Kim, and Sin-Ho Jung
JournalBMC Bioinformatics
Date Published2010 Jul 22
KeywordsAdult, Aged, Aged, 80 and over, Algorithms, Animals, Arthritis, Rheumatoid, Caenorhabditis elegans, Computer Simulation, Gene Expression Profiling, Humans, Middle Aged, Oligonucleotide Array Sequence Analysis, Regression Analysis, Time Factors, Young Adult

BACKGROUND: In a time-course microarray experiment, the expression level for each gene is observed across a number of time-points in order to characterize the temporal trajectories of the gene-expression profiles. For many of these experiments, the scientific aim is the identification of genes for which the trajectories depend on an experimental or phenotypic factor. There is an extensive recent body of literature on statistical methodology for addressing this analytical problem. Most of the existing methods are based on estimating the time-course trajectories using parametric or non-parametric mean regression methods. The sensitivity of these regression methods to outliers, an issue that is well documented in the statistical literature, should be of concern when analyzing microarray data.RESULTS: In this paper, we propose a robust testing method for identifying genes whose expression time profiles depend on a factor. Furthermore, we propose a multiple testing procedure to adjust for multiplicity.CONCLUSIONS: Through an extensive simulation study, we will illustrate the performance of our method. Finally, we will report the results from applying our method to a case study and discussing potential extensions.

Alternate JournalBMC Bioinformatics
Original PublicationRobust test method for time-course microarray experiments.
PubMed ID20649954
PubMed Central IDPMC2914731
Grant ListP01 CA142538 / CA / NCI NIH HHS / United States
CA142538 / CA / NCI NIH HHS / United States