Pathway databases, like Reactome, are uniquely suited for interpreting the results of high-throughput functional genomics data sets such as microarray-based expression profiles, protein interaction sets, and chromatin IP. In response to user feedback and new feature requests, we have released a new Reactome Pathway Browser with an integrated suite of tools for pathway analysis. Using these improved features, you can map protein lists to Reactome pathways, perform pathway overrepresentation analysis for a set of genes, colourize pathway diagrams with gene expression data, and compare model organism and human pathways. To support third-party tool integration, the Reactome Pathway Analysis Portal is also available via RESTful web services. Further details about the new pathway analysis tool can be found in our User Guide.