STATISTICAL ANALYSIS OF MICROARRAY DATA

Goals / Objectives
The objective of this cooperative research project is to use and develop statistical and bioinformatic approaches to analyze the data from microarray assays, and to identify candidate genes for functional studies and genetic markers to isolate the disease resistant genes.

Project Methods
In the collaborative project with Dr. Sally Leong, microarray assays are used to examine gene expression during pathogen infection of rice, barley and finger millet. Statistical and bioinformatic approaches will be used and developed to determine the sequence similarities and conservation of expression patterns among the barley, rice and finger millet genes. Based on conservation of gene expression patterns and sequence similarity the genes, a small set of genes will be selected for their functional studies. In a second project, microarrays are used to study sequence variation among lines of rice and finger millet for identification of single feature polymorphisms (SFPs) that can be used for genetic mapping of disease resistance and genotyping. Various methods of statistical analysis of primary and normalized data will be implemented to identify valid SFPs and minimize detection of false positives. In the collaborative project with Dr. Yong-qiang An, microarray assays are used to examine the expression patterns of more than 20,000 genes over the time course of barley, rice and Arabidopsis germination and seedling growth. Statistical and bioinformatic approaches will be used and developed to determine the sequence similarities and conservation of expression patterns among the barley, rice and Arabidopsis genes. Based on conservation of gene expression patterns and sequence similarity the genes, a small set of genes will be selected for their functional studies.

Progress 09/20/04 to 06/30/06

Outputs
Progress Report 4d Progress report. This report serves to document research conducted under a specific cooperative agreement 3655-22000-015-03S between ARS and the University of Wisconsin. Additional details of research can be found in the report for the parent project 3655-22000-015-00D, Molecular Analysis of Plant Host Recognition of Magnaporthe grisea. No progress was made due to changes in personnel on the project. This project is complete and this is a final report.

Impacts
(N/A)

Publications

Progress 10/01/04 to 09/30/05

Outputs
4d Progress report. This report serves to document research conducted under a specific cooperative agreement 3655-22000-015-03S between ARS and the University of Wisconsin. Additional details of research can be found in the report for the parent project 3655-22000-015-00D, Molecular Analysis of Plant Host Recognition of Magnaporthe grisea. In the project, we developed a bioinformatic approach to compare bio-sequences of over 22,500 barley genes, 57,000 rice genes and 8,200 Arabidopsis genes and identified a large collection of barley, Arabidopsis and rice homologous gene sets, called as BARs. By comparing the expression patterns of barley, rice and Arabidopsis genes in each BAR during germination, we identified 323 BARs that their barley, Arabidopsis and rice homologous genes in each BAR were differentially regulated by germination in a similar pattern. Preserving of the protein sequence, expression patterns and responsiveness to germination since barley, rice and Arabidopsis diverged from their common ancestor about 200 million years ago suggests a functional significance of the 323 BAR genes in germination. The 323 BAR genes may play roles in the biological processes shared by barley, Arabidopsis and rice germination.

Impacts
(N/A)

Publications