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PathwayMatcher is a standalone command line tool to match human biomedical data to pathways. Its advanced mapping functions allow matching multiple types of omics data to the Reactome database: lists of proteoforms, genetic variants, gene or protein identifiers, and lists of peptides including posttranslational modifications.
Please note that PathwayMatcher maps the experimental data to pathways in a systematic and unbiased fashion, without filtering, statistics, or biological inference. We recommend that users interpret the results of the matching using the systems biology method that best suits their experiment and biomedical context.
PathwayMatcher is described here, please use this reference to refer to the tool. The scripts used to generate the figures of the manuscript are available here. We welcome comments and questions on our manuscript, please do not hesitate to contact us via the issue tracker.
PathwayMatcher was presented at the ASHG 2017, the corresponding poster can be found here.
PathwayMatcher is composed by four java project modules called: Extractor, Model, Methods and PathwayMatcher.
- Extractor is the module to gather the reference data to perform the mapping of omics data to pathways from Varian Effect Predictor[1] and Reactome[2].
- Model defines the classes to represent the biological entities handled in the analysis process.
- Methods defines the procedures to search and do pathway analysis.
- PathwayMatcher is the main module with the executable java class to perform the whole process. It employs the other three modules to search and analyise the data.
[1] McLaren, W. et al. The Ensembl Variant Effect Predictor. Genome Biology 17, 122, doi:10.1186/s13059-016-0974-4 (2016).
[2] Fabregat, A. et al. The Reactome Pathway Knowledgebase. Nucleic acids research 46, D649-d655, doi:10.1093/nar/gkx1132 (2018).