{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:42:06Z","timestamp":1753875726954,"version":"3.41.2"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2022,2,11]],"date-time":"2022-02-11T00:00:00Z","timestamp":1644537600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81572935"],"award-info":[{"award-number":["81572935"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Individual pathway analysis can dissect heterogeneities among different cancer patients and provide efficient guidelines for individualized therapy. However, the existence of the batch effect brings extensive limitations for the application of many individual methods for pathway analysis. Previously, researchers proposed that methods based on within-sample relative expression ordering (REO) of the genes are notably insensitive to \u2018batch effects\u2019. In this article, we focus on the Gene Ontology (GO) database and propose an individual qualitative GO term analysis method (IndGOterm) based on the REO of genes. Compared with some current widely used single-sample enrichment analysis methods, such as ssGSEA and GSVA, IndGOterm has a predominance of ignoring the batch effects caused by diverse technologies. Through the survival and drug responses analysis, we found IndGOterm could capture more terms connected to cancer than other single-sample enrichment analysis methods. Furthermore, through the application of IndGOterm, we found some terms that present different dysregulation models that manifest heterogenetic in homologous patients. Collectively, these results attested that IndGOterm could capture useful information from patients and be a useful tool to reveal the intrinsic characteristic of cancer. An open-source R statistical analysis package \u2018IndGOterm\u2019 is available at https:\/\/github.com\/robert19960424\/IndGOterm.<\/jats:p>","DOI":"10.1093\/bib\/bbac012","type":"journal-article","created":{"date-parts":[[2022,1,11]],"date-time":"2022-01-11T12:09:31Z","timestamp":1641902971000},"source":"Crossref","is-referenced-by-count":0,"title":["IndGOterm: a qualitative method for the identification of individually dysregulated GO terms in cancer"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8953-8963","authenticated-orcid":false,"given":"Jiashuai","family":"Zhang","sequence":"first","affiliation":[{"name":"Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huiting","family":"Xiao","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kai","family":"Song","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Keru","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hengrui","family":"Yuan","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rongqiang","family":"Yuan","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jia","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuting","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3252-7961","authenticated-orcid":false,"given":"Zhiqiang","family":"Chang","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wenyuan","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,2,11]]},"reference":[{"key":"2022031506315975200_ref1","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1002375","article-title":"Ten years of pathway analysis: current approaches and outstanding 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