Most of our core genomic and proteomic data analysis functions are now performed using the Rosetta Biosoftware systems Resolver and Elucidator. These systems are designed for managing and analyzing large amounts of gene expression and mass spectrometry data and both contain a suite of higher-order analysis tools. To explore genomic and proteomic data in greater depth, we also use a variety of tools that provide a diversity of analytical choices. As an example, we use Spotfire DecisionSite to format data for further analysis using tools such as Ingenuity Pathway Analysis or MetaCore (GeneGo). These tools allow us to leverage proprietary biological content databases and examine gene expression (or protein abundance) data in the context of complex pathways to identify connections between differentially expressed genes. Sean Proll, Bryan Paeper, and Jon Rue provide the laboratory with expert guidance on the use of these tools and ensure that data moves efficiently through this complex pipeline.