{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:38:34Z","timestamp":1740184714169,"version":"3.37.3"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2020,7,17]],"date-time":"2020-07-17T00:00:00Z","timestamp":1594944000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Turing Research Fellowship under Engineering and Physical Sciences Research Council","award":["TU\/A\/000017"],"award-info":[{"award-number":["TU\/A\/000017"]}]},{"name":"EPSRC\/Biotechnology and Biological Sciences Research Council (BBSRC) Innovation Fellowship","award":["EP\/S001360\/1"],"award-info":[{"award-number":["EP\/S001360\/1"]}]},{"name":"United Kingdom Research and Innovation (UKRI)\/Turing Research Strategic Priority Fund","award":["R-SPES-107"],"award-info":[{"award-number":["R-SPES-107"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,12,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Large gene networks can be dense and difficult to interpret in a biologically meaningful way.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we introduce PAFway, which estimates pairwise associations between functional annotations in biological networks and pathways. It answers the biological question: do genes that have a specific function tend to regulate genes that have a different specific function? The results can be visualized as a heatmap or a network of biological functions. We apply this package to reveal associations between functional annotations in an Arabidopsis thaliana gene network.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>PAFway is submitted to CRAN. Currently available here: https:\/\/github.com\/ezer\/PAFway.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa639","type":"journal-article","created":{"date-parts":[[2020,7,10]],"date-time":"2020-07-10T19:11:36Z","timestamp":1594408296000},"page":"4963-4964","source":"Crossref","is-referenced-by-count":2,"title":["PAFway: pairwise associations between functional annotations in biological networks and pathways"],"prefix":"10.1093","volume":"36","author":[{"given":"Mahiar","family":"Mahjoub","sequence":"first","affiliation":[{"name":"Department of Mathematics, University of Cambridge , Cambridge CB3 0WA, UK"},{"name":"The Alan Turing Institute , London NW1 2DB, UK"},{"name":"Royal Prince Alfred Hospital, Central Clinical School, University of Sydney , Sydney, NSW 2050, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1685-6909","authenticated-orcid":false,"given":"Daphne","family":"Ezer","sequence":"additional","affiliation":[{"name":"The Alan Turing Institute , London NW1 2DB, UK"},{"name":"Department of Statistics, University of Warwick , Coventry CV4 7AL, UK"},{"name":"Department of Biology, University of York , York, YO10 5NG, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,7,17]]},"reference":[{"key":"2023062408054519300_btaa639-B1","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1186\/1471-2105-12-373","article-title":"Quantification of protein group coherence and pathway assignment using functional association","volume":"12","author":"Chitale","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2023062408054519300_btaa639-B2","doi-asserted-by":"crossref","first-page":"D996","DOI":"10.1093\/nar\/gku1053","article-title":"AraNet v2: an improved database of co-functional gene networks for the study of Arabidopsis thaliana and 27 other nonmodel plant species","volume":"43","author":"Lee","year":"2015","journal-title":"Nucleic Acids Res"},{"volume-title":"An information-theoretic definition of similarity","year":"1998","author":"Lin","key":"2023062408054519300_btaa639-B3"},{"key":"2023062408054519300_btaa639-B4","doi-asserted-by":"crossref","first-page":"3448","DOI":"10.1093\/bioinformatics\/bti551","article-title":"BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks","volume":"21","author":"Maere","year":"2005","journal-title":"Bioinformatics"},{"key":"2023062408054519300_btaa639-B5","doi-asserted-by":"crossref","first-page":"278","DOI":"10.3389\/fphys.2013.00278","article-title":"Methods and approaches in the topology-based analysis of biological pathways","volume":"4","author":"Mitrea","year":"2013","journal-title":"Front. 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