{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,17]],"date-time":"2026-01-17T21:16:53Z","timestamp":1768684613147,"version":"3.49.0"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2022,3,10]],"date-time":"2022-03-10T00:00:00Z","timestamp":1646870400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Swedish Research Council Project","award":["2015-05342"],"award-info":[{"award-number":["2015-05342"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,4,28]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Pathway annotation tools are indispensable for the interpretation of a wide range of experiments in life sciences. Network-based algorithms have recently been developed which are more sensitive than traditional overlap-based algorithms, but there is still a lack of good online tools for network-based pathway analysis.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We present PathwAX II\u2014a pathway analysis web tool based on network crosstalk analysis using the BinoX algorithm. It offers several new features compared with the first version, including interactive graphical network visualization of the crosstalk between a query gene set and an enriched pathway, and the addition of Reactome pathways.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>PathwAX II is available at http:\/\/pathwax.sbc.su.se.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac153","type":"journal-article","created":{"date-parts":[[2022,3,9]],"date-time":"2022-03-09T12:24:34Z","timestamp":1646828674000},"page":"2659-2660","source":"Crossref","is-referenced-by-count":10,"title":["PathwAX II: network-based pathway analysis with interactive visualization of network crosstalk"],"prefix":"10.1093","volume":"38","author":[{"given":"Christoph","family":"Ogris","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory , 17121 Solna, Sweden"},{"name":"Institute of Computational Biology, Helmholtz Center Munich , 85764 Neuherberg, Germany"}]},{"given":"Miguel","family":"Castresana-Aguirre","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory , 17121 Solna, Sweden"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9015-5588","authenticated-orcid":false,"given":"Erik L L","family":"Sonnhammer","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory , 17121 Solna, Sweden"}]}],"member":"286","published-online":{"date-parts":[[2022,3,10]]},"reference":[{"key":"2023041402565626000_","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1016\/j.neo.2017.05.003","article-title":"Combined inhibition of CDK4\/6 and PI3K\/AKT\/mTOR pathways induces a synergistic anti-tumor effect in malignant pleural mesothelioma cells","volume":"19","author":"Bonelli","year":"2017","journal-title":"Neoplasia"},{"key":"2023041402565626000_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1155\/2010\/205357","article-title":"Potential role of sugar transporters in cancer and their relationship with anticancer therapy","volume":"2010","author":"Calvo","year":"2010","journal-title":"Int. J. Endocrinol"},{"key":"2023041402565626000_","doi-asserted-by":"crossref","first-page":"3279","DOI":"10.1038\/sj.onc.1210421","article-title":"MAP kinase signalling pathways in cancer","volume":"26","author":"Dhillon","year":"2007","journal-title":"Oncogene"},{"key":"2023041402565626000_","doi-asserted-by":"crossref","first-page":"1537","DOI":"10.1101\/gr.6202607","article-title":"A systems biology approach for pathway level analysis","volume":"17","author":"Draghici","year":"2007","journal-title":"Genome Res"},{"key":"2023041402565626000_","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1186\/1471-2164-11-574","article-title":"Heading down the wrong pathway: on the influence of correlation within gene sets","volume":"11","author":"Gatti","year":"2010","journal-title":"BMC Genomics"},{"key":"2023041402565626000_","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","article-title":"Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources","volume":"4","author":"Huang","year":"2009","journal-title":"Nat. Protoc"},{"key":"2023041402565626000_","first-page":"D481","article-title":"The reactome pathway knowledgebase","volume":"44","author":"Jassal","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023041402565626000_","doi-asserted-by":"crossref","first-page":"1739","DOI":"10.1093\/bioinformatics\/btr260","article-title":"Molecular signatures database (MSigDB) 3.0","volume":"27","author":"Liberzon","year":"2011","journal-title":"Bioinformatics"},{"key":"2023041402565626000_","doi-asserted-by":"crossref","first-page":"2970","DOI":"10.1158\/0008-5472.CAN-05-3907","article-title":"Global gene expression profiling of pleural mesotheliomas: overexpression of aurora kinases andP16\/CDKN2ADeletion as prognostic factors and critical evaluation of microarray-based prognostic prediction","volume":"66","author":"L\u00f3pez-R\u00edos","year":"2006","journal-title":"Cancer Res"},{"key":"2023041402565626000_","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1007\/s10555-014-9498-0","article-title":"Platelets and cancer: a casual or causal relationship: revisited","volume":"33","author":"Menter","year":"2014","journal-title":"Cancer Metastasis Rev"},{"key":"2023041402565626000_","doi-asserted-by":"crossref","first-page":"e8","DOI":"10.1093\/nar\/gkw849","article-title":"A novel method for crosstalk analysis of biological networks: improving accuracy of pathway annotation","volume":"45","author":"Ogris","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023041402565626000_","doi-asserted-by":"crossref","first-page":"D601","DOI":"10.1093\/nar\/gkx1138","article-title":"FunCoup 4: new species, data, and visualization","volume":"46","author":"Ogris","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023041402565626000_","doi-asserted-by":"crossref","first-page":"W105","DOI":"10.1093\/nar\/gkw356","article-title":"PathwAX: a web server for network crosstalk based pathway annotation","volume":"44","author":"Ogris","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023041402565626000_","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1007\/978-1-60327-241-4_8","article-title":"Biomolecular pathway databases","volume":"609","author":"Ooi","year":"2010","journal-title":"Methods Mol. Biol"},{"key":"2023041402565626000_","doi-asserted-by":"crossref","first-page":"451084","DOI":"10.1155\/2009\/451084","article-title":"Mesothelioma cells escape heat stress by upregulating Hsp40\/Hsp70 expression via mitogen-activated protein kinases","volume":"2009","author":"Roth","year":"2009","journal-title":"J. Biomed. Biotechnol"},{"key":"2023041402565626000_","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023041402565626000_","doi-asserted-by":"crossref","first-page":"D607","DOI":"10.1093\/nar\/gky1131","article-title":"STRING v11: protein\u2013protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets","volume":"47","author":"Szklarczyk","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023041402565626000_","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1186\/1471-2105-13-136","article-title":"Down-weighting overlapping genes improves gene set analysis","volume":"13","author":"Tarca","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2023041402565626000_","doi-asserted-by":"crossref","first-page":"1260419","DOI":"10.1126\/science.1260419","article-title":"Tissue-based map of the human proteome","volume":"347","author":"Uhlen","year":"2015","journal-title":"Science"},{"key":"2023041402565626000_","doi-asserted-by":"crossref","first-page":"2479","DOI":"10.1038\/bjc.2014.220","article-title":"Multipoint targeting of the PI3K\/mTOR pathway in mesothelioma","volume":"110","author":"Zhou","year":"2014","journal-title":"Br. J. Cancer"},{"key":"2023041402565626000_","doi-asserted-by":"crossref","first-page":"W115","DOI":"10.1093\/nar\/gkt533","article-title":"GeneMANIA prediction server 2013 update","volume":"41","author":"Zuberi","year":"2013","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac153\/43192441\/btac153.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/9\/2659\/49874438\/btac153.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/9\/2659\/49874438\/btac153.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,18]],"date-time":"2023-11-18T16:28:25Z","timestamp":1700324905000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/9\/2659\/6546284"}},"subtitle":[],"editor":[{"given":"Pier Luigi","family":"Martelli","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,3,10]]},"references-count":21,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2022,4,28]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac153","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,5,1]]},"published":{"date-parts":[[2022,3,10]]}}}