D694 Nucleic Acids Research, 2011, Vol. 39, Database issue molecular interaction (MI) data and network information into the Reactome pathway diagrams (Figure 1). The MI overlay displays proteins interacting with the manually annotated protein components of a Reactome pathway. As mentioned previously, individual protein interactors can be displayed using the context-dependent menus in the pathway ‘Visualization’ workspace. It is also possible to overlay all the interactors for all the pathway proteins by means of the ‘Analyze, Annotate and Upload’ feature of the Pathway Browser. The network overlay tool employs a PSICQUIC interface to implement ﬂexible import of binary MI data into Reactome pathway diagrams. PSICQUIC is already widely implemented by interaction databases, including BioGRID, ChEMBL, IntAct, iRefIndex, MINT and STRING (15–20). The nodes and edges of the network overlay are interactive, providing links to the physical entity and interaction databases, re- spectively. Two of additional interaction data sets are managed by the Reactome group, ‘Reactome’ and ‘Reactome-FIs’. The original ‘Reactome’ data set reﬂects MI data derived from Reactome reactions and complexes. A new ‘Reactome-FIs’ (functional interactions) data set unites interactions from Reactome and those derived from other pathway databases, including KEGG, BioCyc, Panther, The Cancer Cell Map (http://cancer. cellmap.org/) and PID (7,21–23) with pair-wise inter- actions gleaned from physical protein–protein interactions in human and model organisms, gene co-expression data, protein domain–domain interactions, protein interactions generated from text mining and GO annotations (24). The ‘Reactome-FIs’ network contains 209 988 functional inter- actions encompassing 10 956 proteins (excluding splice isoforms), reﬂecting 46% of SwissProt proteins. Improved orthology prediction and visualization of predicted pathways for model organisms Comparative analysis of biological processes offers im- portant information on their evolution, and supports metabolic engineering, the study of human disease and the identiﬁcation of potential drug targets. Curated human reactions were used previously to electronically infer reactions by orthology in 20 evolutionary divergent species, with the assistance of the OrthoMCL (25). To align Reactome more closely with the Ensembl set of genome data and genome analysis tools, we have shifted to Ensembl Compara (26) to support orthology-based reaction inferences in 20 species for which high-quality whole-genome sequence data are available, including all 12 of the species in the GO Reference Genome annotation project (27). Viewing diagrams for predicted pathways in another species are available from within the Pathway Browser (Figure 2). A new Species Comparison tool allows users to compare these predicted pathways with Figure 2. Species comparison tool and model organism pathway diagrams. (A) A drop-down menu is used to select the model organism species. (B) Results for the comparison of human and mouse pathways. Each row in the table is a pathway; the columns are pathway name, model organism name, number of proteins in the human pathway, number of orthologous proteins in the inferred model organism pathway, a graphical represen- tation of the ratio of these two values and a ‘View’ button that creates a pathway diagram. ‘Sort’ buttons at the top of each column allow the table to be re-ordered according to cell contents in that column. (C) The pathway browser displaying the comparison of the human and mouse Mitotic M-M/G1 pathways. Physical entities in the pathway diagram are color-coded: gray, no match; black, a complex (multicomponent) entity; and yellow, the protein’s ortholog is present in human. (D) The pathway browser displaying the inferred mouse Mitotic M-M/G1 pathway.