Sorin Draghici and colleagues at Wayne State University School of Medicine have developed a software tool, Onto-Express, that maps differentially regulated genes in a microarray experiment to their function. The user enters into the program a list of accession numbers, UniGene cluster IDs or Affy probe IDs, Draghici said. The software then compiles a list that includes the functional categories associated with each gene, as well as statistics showing how many genes fit into each functional category. The categories include: biological process, cellular role, biochemical function, chromosome location; cellular component, and molecular function. This and other tools are available free at http://vortex.cs.wayne.edu/Projects.html
The European Bioinformatics Institute has released a beta version of MIAMExpress, a web-based submission tool for its public microarray database, ArrayExpress. The tool walks user through the requirements set by the Microarray Gene Expression Database working group, the minimum information about a microarray experiment, to ensure that submissions comply with this standard. EBI encourages users to practice using the tool, even though it is “not perfect yet,” according to Alvis Brazma, team leader of the EBI’s microarray informatics group at EBI.
ArrayExpress (www.ebi.uk/ microarray/ArrayExpress) accepts three kinds of submissions — hybridization data sets, laboratory and data processing protocols, and array design.