Design & Analysis of Microarray Gene Expression Studies in Plants: Toward Sound Statistical Procedures

University Of Alabama At Birmingham, Birmingham AL

Investigators

Abstract

Microarrays are a powerful new technology offering plant biologists the opportunity the measure the expression of thousands of genes simultaneously. This potentially allows plant biologists to make major leaps forward by increasing the number of factors they can examine and offering the opportunity to study the complex relations and physiological coordination among entire genomes. For this technology to achieve its potential, a richer understanding of the statistical properties of the data produced and statistically sound methods for analyzing those data must be developed and made available. Unfortunately, many statistical procedures currently used in microarray research do not have a sound statistical foundation. This research will contribute novel statistical techniques to the microarray field that are, in all cases, rigorously validated by either mathematical proofs or computer simulations. Methods will be developed in three areas: Measurement & Estimation, Design, & Inference. Methods will be tested on real and simulated data. Software for all methods developed will be publicly available. A plan to educate and inform students, plant biologists and statisticians about the methods will be implemented including a short course held at a National plant biology meeting in year 4. The investigative team includes a cadre of investigators with track records in organizing large collaborative efforts, developing novel statistical techniques, and disseminating methods through educational activities and quality software. The investigative team is complemented by a blue-ribbon panel Advisory Committee with expertise in plant biology, microarrays, and computer science. Historically, plants of economic importance (e.g., maize, soy, wheat, pine) have been critical to our country's prosperity and growth. Today, America's strength in supplying food of high nutritional value for human and livestock consumption, cash crops for sale and export, and plant materials for construction remains critical. Indeed, as the world population grows, the ability to produce plants for nutrition and construction materials with tightening resources in a broadening range of environments will be essential. Given their potential to rapidly advance understanding of basic plant biology, microarrays can enhance the ability to produce plants with increased efficiency and enhanced characteristics in the greatest range of environments. Developing valid techniques and facilitating use via quality software and systematic dissemination and educational activities as will be done here can have greatly amplified impact by providing tools of use to the more than 100 other NSF-funded microarray grants and the vast ongoing microarray research world-wide.