Comparing functional genomic datasets: lessons from DNA. microarray analyses of host-pathogen interactions

Functional genomic technologies such as high density DNA microarrays allow biologists to study the structure and behavior of thousands of genes in a s ingle experiment. One of the fields in which microarrays have had an increa singly important impact is host-pathogen interactions. Early investigations in this area over the past two years not only emphasize the utility of thi s approach, but also highlight the stereotyped gene expression responses of different host cells to diverse infectious stimuli, and the potential valu e of broad dataset comparisons in revealing fundamental features of innate immunity. The comparative analysis of recently published datasets involving human gene expression responses to two bacterial respiratory pathogens ill ustrates many of these points. Comparisons between these large, highly para llel sets of experimental observations also emphasize important technical a nd experimental design issues as future challenges.