Screen shots of BMDExpress software application. The software uses standard drop-down windows for user interaction and the left-hand side of the main window contains a tree structure that outlines progress through the analysis process. (A) Interface for data import. The data is previewed in table format and if the input data has column headers, the user is provided the option to remove headers within the software interface. (B) Interface for pre-filtering data using a one-way ANOVA. The user is allowed to input an adjusted p-cutoff and select whether to filter out the various control genes (e.g., BioB, BioC, etc.) present on an Affymetrix array. (C) Interface for benchmark dose analysis. The user is allowed to select the type of statistical models and parameters used in the analysis and provided options on the process of selecting the best model. (D) Interface for gene ontology analysis. The BMD values from the previous step in the analysis process are used as input for the gene ontology analysis. The organism is automatically detected by the software based on the probe set identifiers. The user is allowed to select the class of gene ontology categories for the analysis with either biological process, molecular function, cell component, or universal (all three) as options.