The invention relates to methods and systems (e.g., computer systems and computer program products) for determining the biological function of uncharacterized cellular constituents, particularly genes and gene products, by using “response profiles,” i.e., measurements of pluralities of cellular constituents in cells having a modified gene or gene product, as phenotypic markers for the gene or gene product. Methods are provided for clustering such response profiles so that similar or correlated response profiles are organized into the same cluster. The invention also provides databases or “compendiums” of response profiles to which the response profile of an uncharacterized gene or gene product can be compared. In one embodiment, steps of the methods comprise comparing the measured response profiles to response profiles stored in the databases or compendiums, and determining the biological function of the response profiles in the databases that are most similar to the measured response profiles.