Computational strategies for analyzing data in gene expression microarray experiments.
Microarray analysis has become a widely used method for generating gene expression data on a genomic scale. Microarrays have been enthusiastically applied in many fields of biological research, even though several open questions remain about the analysis of such data. A wide range of approaches are available for computational analysis, but no general consensus exists as to standard for microarray data analysis protocol. Consequently, the choice of data analysis technique is a crucial element depending both on the data and on the goals of the experiment. Therefore, basic understanding of bioinformatics is required for optimal experimental design and meaningful interpretation of the results. This review summarizes some of the common themes in DNA microarray data analysis, including data normalization and detection of differential expression. Algorithms are demonstrated by analyzing cDNA microarray data from an experiment monitoring gene expression in T helper cells. Several computational biology strategies, along with their relative merits, are overviewed and potential areas for additional research discussed. The goal of the review is to provide a computational framework for applying and evaluating such bioinformatics strategies. Solid knowledge of microarray informatics contributes to the implementation of more efficient computational protocols for the given data obtained through microarray experiments.
Aittokallio
Tero
T
Department of Computational Biology, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-Shi, Chiba 277-8562, Japan. jun@gi.k.u-tokyo.ac.jp
Kurki
Markus
M
Nevalainen
Olli
O
Nikula
Tuomas
T
West
Anne
A
Lahesmaa
Riitta
R
D000465:Algorithms; D019295:Computational Biology; D003627:Data Interpretation, Statistical; D020869:Gene Expression Profiling / Q000592:standards / Q000706:statistics & numerical data*; D006801:Humans; D007091:Image Processing, Computer-Assisted; D020411:Oligonucleotide Array Sequence Analysis / Q000592:standards / Q000706:statistics & numerical data*; D011786:Quality Control; D006377:T-Lymphocytes, Helper-Inducer / Q000276:immunology / Q000378:metabolism