{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,26]],"date-time":"2026-06-26T07:34:48Z","timestamp":1782459288078,"version":"3.54.5"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2020,11,24]],"date-time":"2020-11-24T00:00:00Z","timestamp":1606176000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"PKU-Baidu Fund","award":["2019BD012"],"award-info":[{"award-number":["2019BD012"]}]},{"DOI":"10.13039\/501100009592","name":"Beijing Municipal Science and Technology Commission","doi-asserted-by":"publisher","award":["Z201100008320006"],"award-info":[{"award-number":["Z201100008320006"]}],"id":[{"id":"10.13039\/501100009592","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005088","name":"Beijing Municipal Bureau of Health","doi-asserted-by":"publisher","award":["2019-1"],"award-info":[{"award-number":["2019-1"]}],"id":[{"id":"10.13039\/501100005088","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Protein\u2013protein interactions (PPIs) are crucial to mediate biological functions, and understanding PPIs in cancer type-specific context could help decipher the underlying molecular mechanisms of tumorigenesis and identify potential therapeutic options. Therefore, we update the Protein Interaction Network Analysis (PINA) platform to version 3.0, to integrate the unified human interactome with RNA-seq transcriptomes and mass spectrometry-based proteomes across tens of cancer types. A number of new analytical utilities were developed to help characterize the cancer context for a PPI network, which includes inferring proteins with expression specificity and identifying candidate prognosis biomarkers, putative cancer drivers, and therapeutic targets for a specific cancer type; as well as identifying pairs of co-expressing interacting proteins across cancer types. Furthermore, a brand-new web interface has been designed to integrate these new utilities within an interactive network visualization environment, which allows users to quickly and comprehensively investigate the roles of human interacting proteins in a cancer type-specific context. PINA is freely available at https:\/\/omics.bjcancer.org\/pina\/.<\/jats:p>","DOI":"10.1093\/nar\/gkaa1075","type":"journal-article","created":{"date-parts":[[2020,10,23]],"date-time":"2020-10-23T11:32:10Z","timestamp":1603452730000},"page":"D1351-D1357","source":"Crossref","is-referenced-by-count":54,"title":["PINA 3.0: mining cancer interactome"],"prefix":"10.1093","volume":"49","author":[{"given":"Yang","family":"Du","sequence":"first","affiliation":[{"name":"Center for Cancer Bioinformatics, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing\u00a0100142, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meng","family":"Cai","sequence":"additional","affiliation":[{"name":"Institute of Systems Biomedicine, Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing\u00a0100191, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaofang","family":"Xing","sequence":"additional","affiliation":[{"name":"Department of Gastrointestinal Translational Research, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing\u00a0100142, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6878-5543","authenticated-orcid":false,"given":"Jiafu","family":"Ji","sequence":"additional","affiliation":[{"name":"Gastrointestinal Cancer Center, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing\u00a0100142, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ence","family":"Yang","sequence":"additional","affiliation":[{"name":"Institute of Systems Biomedicine, Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing\u00a0100191, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8876-128X","authenticated-orcid":false,"given":"Jianmin","family":"Wu","sequence":"additional","affiliation":[{"name":"Center for Cancer Bioinformatics, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing\u00a0100142, China"},{"name":"Peking University International Cancer Institute, Peking University, Beijing\u00a0100191, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,11,24]]},"reference":[{"key":"2021010313123373100_B1","doi-asserted-by":"crossref","first-page":"e1002690","DOI":"10.1371\/journal.pcbi.1002690","article-title":"Enhancing the prioritization of disease-causing genes through tissue specific protein interaction networks","volume":"8","author":"Magger","year":"2012","journal-title":"PLoS Comput. 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