Ortho2ExpressMatrix workflow and usage. Several different formats of the user's data are accepted by the web tool that allows the entry at several stages of the processing pipeline (step 1, input). Input data comprise either expression values for treatment and control or respective expression ratios of each of the two organisms or individuals to be compared. The processing, shown in step 2, covers the gene annotation levels from probe sets across transcript, protein to protein family annotation. Here, several external sources are named such as EnsemblCompara, InParanoid, SYSTERS, Ensembl Families for protein family approaches. The other annotation associations are derived, mainly from Ensembl, for the five species human, mouse, fruit fly, worm and yeast. Step 3 symbolizes the web server output (A) as matrix visualization and (B) as table. Similarly to the shown protein family association, the tool performs the association task also for family information of microRNAs.