Microarray profiling of gene expression is a powerful tool for discovery, but the ability to manage and compare the resulting data can be problematic. Biological, experimental, and technical variations between studies of the same phenotype/phenomena create substantial differences in results. The application of conventional meta-analysis to raw microarray data is complicated by differences in the type of microarray used, gene nomenclatures, species, and analytical methods. An alternative approach to combining multiple microarray studies is to compare the published gene lists which result from the investigators' analyses of the raw data, as implemented in Lists of Lists Annotated (LOLA: www.lola.gwu.edu) and L2L (depts.washington.edu/l2l/). The present review considers both the potential value and the limitations of databasing and enabling the comparison of results from different microarray studies. Further, a major impediment to cross-study comparisons is the absence of a standard for reporting microarray study results. We propose a reporting standard: standard microarray results template (SMART), which will facilitate the integration of microarray studies.
Picky is an efficient oligo microarray design tool for large genomes. Picky integrates novel computer science techniques and the best known nearest-neighbor parameters to quickly identify sequence similarities and estimate their hybridization properties. Oligos designed by Picky are computationally optimized to guarantee the best specificity, sensitivity and uniformity under the given design constrains. Picky can be used to design arrays for whole genomes, or for only a subset of genes. The latter can still be screened against a whole genome to attain the same quality as a whole genome array, thereby permitting low budget, pathway-specific experiments to be conducted with large genomes. Picky is the fastest oligo array design tool currently available to the public, requiring only a few hours to process large gene sets from rice, maize or human.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.