{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,6]],"date-time":"2025-11-06T06:17:16Z","timestamp":1762409836626,"version":"3.37.3"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"22-23","license":[{"start":{"date-parts":[[2020,12,1]],"date-time":"2020-12-01T00:00:00Z","timestamp":1606780800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Although several bioinformatics tools have been developed to examine signaling pathways, little attention has been given to ever long-distance crosstalk mechanisms. Here, we developed PETAL, a Python tool that automatically explores and detects the most relevant nodes within a KEGG pathway, scanning and performing an in-depth search. PETAL can contribute to discovering novel therapeutic targets or biomarkers that are potentially hidden and not considered in the network under study.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availabilityand implementation<\/jats:title>\n                  <jats:p>PETAL is a freely available open-source software. It runs on all platforms that support Python3. The user manual and source code are accessible from https:\/\/github.com\/Pex2892\/PETAL.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa1032","type":"journal-article","created":{"date-parts":[[2020,12,1]],"date-time":"2020-12-01T13:15:12Z","timestamp":1606828512000},"page":"5553-5555","source":"Crossref","is-referenced-by-count":4,"title":["PETAL: a Python tool for deep analysis of biological pathways"],"prefix":"10.1093","volume":"36","author":[{"given":"Giuseppe","family":"Sgroi","sequence":"first","affiliation":[{"name":"Department of Mathematics and Computer Science, University of Catania , 95125 Catania, Italy"}]},{"given":"Giulia","family":"Russo","sequence":"additional","affiliation":[{"name":"Depatment of Drug Sciences, University of Catania , 95125 Catania, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1668-3320","authenticated-orcid":false,"given":"Francesco","family":"Pappalardo","sequence":"additional","affiliation":[{"name":"Depatment of Drug Sciences, University of Catania , 95125 Catania, Italy"}]}],"member":"286","published-online":{"date-parts":[[2020,12,16]]},"reference":[{"key":"2023062707304757900_btaa1032-B1","doi-asserted-by":"crossref","first-page":"2301","DOI":"10.1109\/TVCG.2011.185","article-title":"D3 data-driven documents","volume":"17","author":"Bostock","year":"2011","journal-title":"IEEE Trans. Vis. Comput. Graph"},{"key":"2023062707304757900_btaa1032-B2","doi-asserted-by":"crossref","first-page":"174","DOI":"10.3389\/fgene.2017.00174","article-title":"A review of pathway-based analysis tools that visualize genetic variants","volume":"8","author":"Cirillo","year":"2017","journal-title":"Front. Genet"},{"key":"2023062707304757900_btaa1032-B3","doi-asserted-by":"crossref","first-page":"D649","DOI":"10.1093\/nar\/gkx1132","article-title":"The Reactome Pathway Knowledgebase","volume":"46","author":"Fabregat","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023062707304757900_btaa1032-B4","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1093\/bioinformatics\/btv557","article-title":"Cytoscape.js: a graph theory library for visualisation and analysis","volume":"32","author":"Franz","year":"2015","journal-title":"Bioinformatics"},{"key":"2023062707304757900_btaa1032-B5","doi-asserted-by":"crossref","first-page":"2267","DOI":"10.1093\/bioinformatics\/bty969","article-title":"Computational modeling reveals MAP3K8 as mediator of resistance to vemurafenib in thyroid cancer stem cells","volume":"35","author":"Gian\u00ec","year":"2019","journal-title":"Bioinformatics"},{"key":"2023062707304757900_btaa1032-B6","doi-asserted-by":"crossref","first-page":"277D","DOI":"10.1093\/nar\/gkh063","article-title":"The KEGG resource for deciphering the genome","volume":"32","author":"Kanehisa","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2023062707304757900_btaa1032-B7","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1109\/MITP.2005.120","article-title":"Programming with Python","volume":"7","author":"Lindstrom","year":"2005","journal-title":"IT Prof"},{"key":"2023062707304757900_btaa1032-B8","doi-asserted-by":"crossref","first-page":"a011254","DOI":"10.1101\/cshperspect.a011254","article-title":"MAP kinase pathways","volume":"4","author":"Morrison","year":"2012","journal-title":"Cold Spring Harb. 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