Enriched ontology bins by metal.

Bins were created to identify the function of a large number of differentially expressed genes and are based on known effects of nickel, chromium and cadmium. Probe sets are assigned to bins based on gene ontology biological process terms. A chi-squared test was used to determine whether the proportion of probe sets in a bin due to metal exposure differed from the proportion of probe sets in each bin based on probe sets having a “present” call (see Methods) in the data set and at least one ontology term from the relevant bin. The oxidative stress bin was enriched in response to all three metals, while a large proportion of probe sets modulated by chromium were assigned to the DNA damage bin, and nickel enriched the hypoxic response and energy regulation bins.