Modern health initiatives and drug discovery are focused increasingly on targeting diseases that arise from perturbations in complex cellular events. Consequently, there has been a tremendous effort in biological research to elucidate the molecular mechanisms that underpin normal cellular processes. A reaction-network pathway knowledgebase is the tool of choice for assembling and visualizing the “parts list” of proteins and functional RNAs, as a foundation for understanding cellular processes, function and disease. The Reactome Knowledgebase (www.reactome.org) is a publically accessible, open access bioinformatics resource that stores full descriptions of human biological reactions, pathways and processes. Curated pathway knowledgebases, like Reactome, are uniquely powerful and flexible tools for extracting biologically and clinically useful information from the flood of genomic data. Our data model accommodates the annotation of disease processes, allowing us to represent the altered biological behaviour of mutant variants frequently found in cancer, and to describe the mode of action and specificity of drugs and therapeutics. Bio- and chemoinformaticians use Reactome to interpret high-throughput experimental datasets, to develop novel algorithms for data mining and visualization, and to build predictive models of normal and abnormal pathways. Specific features of Reactome support the visualization of interactions of many gene products in a complex biological process, and the application of bioinformatics tools to find causal patterns in genomic data sets. To maximize Reactome’s coverage of the genome, we have supplemented curated data with a conservative set of predicted functional interactions (FI), roughly doubling our coverage of the translated genome. We have developed a Cytoscape app called “ReactomeFIViz”, which utilizes this FI network to assist biologists to perform pathway and network analysis to search for gene signatures from within gene expression data sets or identify significant genes within a list. Pathway and network-based tools for building and validating interaction networks derived from multiple data sets will give researchers substantial power to screen intrinsically noisy experimental data in order to uncover biologically relevant information.

Reactome pathway knowledgebase: Connecting pathways, networks, and disease

251st National Meeting (2016)

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