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PathDIP 4 now integrates 24 major databases. To further reduce the number of proteins with no curated pathway annotation, pathDIP integrates pathways with physical protein\u2013protein interactions (PPIs) to predict significant physical associations between proteins and curated pathways. For human, it provides pathway annotations for 5366 pathway orphans. Integrated pathway annotation now includes six model organisms and ten domesticated animals. A total of 6401 core and ortholog pathways have been curated from the literature or by annotating orthologs of human proteins in the literature-curated pathways. Extended pathways are the result of combining these pathways with protein-pathway associations that are predicted using organism-specific PPIs. Extended pathways expand proteome coverage from 81 088 to 120 621 proteins, making pathDIP 4 the largest publicly available pathway database for these organisms and providing a necessary platform for comprehensive pathway-enrichment analysis. PathDIP 4 users can customize their search and analysis by selecting organism, identifier and subset of pathways. Enrichment results and detailed annotations for input list can be obtained in different formats and views. To support automated bioinformatics workflows, Java, R and Python APIs are available for batch pathway annotation and enrichment analysis. PathDIP 4 is publicly available at http:\/\/ophid.utoronto.ca\/pathDIP.<\/jats:p>","DOI":"10.1093\/nar\/gkz989","type":"journal-article","created":{"date-parts":[[2019,11,13]],"date-time":"2019-11-13T20:09:37Z","timestamp":1573675777000},"source":"Crossref","is-referenced-by-count":17,"title":["pathDIP 4: an extended pathway annotations and enrichment analysis resource for human, model organisms and domesticated species"],"prefix":"10.1093","author":[{"given":"Sara","family":"Rahmati","sequence":"first","affiliation":[{"name":"Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada"},{"name":"Department of Medicine, Toronto Western Hospital, University Health Network, Toronto, ON M5T 2S8, Canada"},{"name":"Department of Medicine, Memorial University of Newfoundland, Saint John's, NL A1B 3V6, Canada"}]},{"given":"Mark","family":"Abovsky","sequence":"additional","affiliation":[{"name":"Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, 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University Health Network, Toronto, ON M5T 0S8, Canada"},{"name":"Department of Medicine, Toronto Western Hospital, University Health Network, Toronto, ON M5T 2S8, Canada"},{"name":"Department of Medicine, Memorial University of Newfoundland, Saint John's, NL A1B 3V6, Canada"},{"name":"Department of Medicine, Division of Rheumatology, University of Toronto, Toronto, ON M5G 2C4, Canada"},{"name":"Department of Laboratory Medicine and Pathobiology (LMP), Medicine, University of Toronto, Toronto, ON M5S 1A8, Canada"}]},{"given":"Igor","family":"Jurisica","sequence":"additional","affiliation":[{"name":"Krembil Research Institute, University Health Network, Toronto, ON M5T 0S8, Canada"},{"name":"Department of Medical Biophysics, University of Toronto, ON M 5G 1L7, Canada"},{"name":"Department of Computer Science, University of Toronto, ON M5S 1A4, Canada"},{"name":"Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, 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