{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,19]],"date-time":"2025-10-19T15:43:48Z","timestamp":1760888628130},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Gene therapy aims at using viral vectors for attaching helpful genetic code to target genes. Therefore, it is of great importance to develop methods that can discover significant patterns around viral integration sites. Canonical correlation analysis is an unsupervised statistical tool that is used to describe the relations between two related views of the same semantic object, which fits well for identifying such salient patterns.<\/jats:p>\n               <jats:p>Results: Proposed method is demonstrated on a sequence dataset obtained from a study on HIV-1 preferred integration regions. The subsequences on the left and right sides of the integration points are given to the method as the two views, and statistically significant relations are found between sequence-driven features derived from these two views, which suggest that the viral preference must be the factor responsible for this correlation. We found that there are significant correlations at x=5 indicating a palindromic behavior surrounding the viral integration site, which complies with the previously reported results.<\/jats:p>\n               <jats:p>Availability: Developed software tool is available at http:\/\/ce.istanbul.edu.tr\/bioinformatics\/hiv1\/<\/jats:p>\n               <jats:p>Contact: \u00a0egumus@istanbul.edu.tr<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts027","type":"journal-article","created":{"date-parts":[[2012,1,14]],"date-time":"2012-01-14T01:50:47Z","timestamp":1326505847000},"page":"651-655","source":"Crossref","is-referenced-by-count":16,"title":["Application of canonical correlation analysis for identifying viral integration preferences"],"prefix":"10.1093","volume":"28","author":[{"given":"Ergun","family":"Gumus","sequence":"first","affiliation":[{"name":"1 Department of Computer Engineering, Istanbul University, Istanbul 34320 Turkey and 2Department of Genetics, Institute for Experimental Medicine, Istanbul University, Istanbul 34093 Turkey"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olcay","family":"Kursun","sequence":"additional","affiliation":[{"name":"1 Department of Computer Engineering, Istanbul University, Istanbul 34320 Turkey and 2Department of Genetics, Institute for Experimental Medicine, Istanbul University, Istanbul 34093 Turkey"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ahmet","family":"Sertbas","sequence":"additional","affiliation":[{"name":"1 Department of Computer Engineering, Istanbul University, Istanbul 34320 Turkey and 2Department of Genetics, Institute for Experimental Medicine, Istanbul University, Istanbul 34093 Turkey"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Duran","family":"Ustek","sequence":"additional","affiliation":[{"name":"1 Department of Computer Engineering, Istanbul University, Istanbul 34320 Turkey and 2Department of Genetics, Institute for Experimental Medicine, Istanbul University, Istanbul 34093 Turkey"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2012,1,12]]},"reference":[{"key":"2023012512193677100_B1","volume-title":"A canonical correlation approach to blind source separation.","author":"Borga","year":"2001"},{"key":"2023012512193677100_B2","doi-asserted-by":"crossref","first-page":"e17293","DOI":"10.1371\/journal.pone.0017293","article-title":"A novel method of characterizing genetic sequences: genome space with biological distance and applications","volume":"6","author":"Deng","year":"2011","journal-title":"PLoS One"},{"key":"2023012512193677100_B3","doi-asserted-by":"crossref","first-page":"608","DOI":"10.1093\/bioinformatics\/17.7.608","article-title":"Identifying target sites for cooperatively binding factors","volume":"17","author":"GuhaThakurta","year":"2001","journal-title":"Bioinformatics"},{"key":"2023012512193677100_B4","doi-asserted-by":"crossref","first-page":"2639","DOI":"10.1162\/0899766042321814","article-title":"Canonical correlation analysis: an overview with application to learning methods","volume":"16","author":"Hardoon","year":"2004","journal-title":"Neural Computation"},{"key":"2023012512193677100_B5","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1093\/bioinformatics\/15.7.563","article-title":"Identifying DNA and protein patterns with statistically significant alignments of multiple sequences","volume":"15","author":"Hertz","year":"1999","journal-title":"Bioinformatics"},{"key":"2023012512193677100_B6","doi-asserted-by":"crossref","first-page":"6103","DOI":"10.1073\/pnas.0501646102","article-title":"Symmetrical base preferences surrounding HIV-1, avian sarcoma\/leucosis virus, and murine leukemia virus integration sites","volume":"102","author":"Holman","year":"2005","journal-title":"Proc. Nal Acad. Sci. USA"},{"key":"2023012512193677100_B7","doi-asserted-by":"crossref","DOI":"10.1007\/978-0-387-78189-1","volume-title":"Modern Multivariate Statistical Techniques: Regression, Classification, and Manifold Learning. Springer Texts in Statistics","author":"Izenman","year":"2008","edition":"1st"},{"key":"2023012512193677100_B8","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1016\/j.patrec.2010.09.025","article-title":"Canonical Correlation Analysis Using Within-class Coupling","volume":"32","author":"Kursun","year":"2011","journal-title":"Pattern Recogn. Lett."},{"key":"2023012512193677100_B9","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1126\/science.8211139","article-title":"Detecting subtle sequence signals: Gibbs sampling strategy for multiple alignment","volume":"262","author":"Lawrence","year":"1993","journal-title":"Science"},{"issue":"Suppl. 2","key":"2023012512193677100_B10","doi-asserted-by":"crossref","first-page":"W32","DOI":"10.1093\/nar\/gkl305","article-title":"PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence","volume":"34","author":"Li","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012512193677100_B11","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1089\/106652703322756113","article-title":"Combining pairwise sequence similarity and support vector machines for detecting remote protein evolutionary and structural relationships","volume":"10","author":"Liao","year":"2003","journal-title":"J. Comput. Biol."},{"key":"2023012512193677100_B12"},{"key":"2023012512193677100_B13","doi-asserted-by":"crossref","first-page":"e10395","DOI":"10.1371\/journal.pone.0010395","article-title":"Using canonical correlation analysis to discover genetic regulatory variants","volume":"5","author":"Naylor","year":"2010","journal-title":"PLoS ONE"},{"key":"2023012512193677100_B14","doi-asserted-by":"crossref","first-page":"1","DOI":"10.2202\/1544-6115.1406","article-title":"Sparse canonical correlation analysis with application to genomic data integration","volume":"8","author":"Parkhomenko","year":"2009","journal-title":"Stat. Appl. Genet. Mol. Biol."},{"key":"2023012512193677100_B15","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1038\/ejhg.2009.223","article-title":"A gene-based method for detecting gene-gene co-association in a case-control association study","volume":"18","author":"Peng","year":"2010","journal-title":"Eur. J. Hum. Genet."},{"key":"2023012512193677100_B16","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1016\/S0092-8674(02)00864-4","article-title":"HIV-1 integration in the human genome favors active genes and local hotspots","volume":"110","author":"Schroder","year":"2002","journal-title":"Cell"},{"key":"2023012512193677100_B17","first-page":"105","article-title":"Prediction of protein subcellular localizations using moment descriptors and support vector machine","volume-title":"Lecture Notes in Computer Science","author":"Shi","year":"2006"},{"key":"2023012512193677100_B18","volume-title":"Basic Statistical Analysis","author":"Sprinthall","year":"2003","edition":"7th"},{"key":"2023012512193677100_B19","doi-asserted-by":"crossref","first-page":"5211","DOI":"10.1128\/JVI.79.8.5211-5214.2005","article-title":"Weak palindromic consensus sequences are a common feature found at the integration target sites of many retroviruses","volume":"79","author":"Wu","year":"2005","journal-title":"J. Virol."},{"issue":"1\u20132","key":"2023012512193677100_B20","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1089\/10665270050081478","article-title":"A greedy algorithm for aligning DNA sequences","volume":"7","author":"Zhang","year":"2000","journal-title":"J. Comput. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/5\/651\/48881557\/bioinformatics_28_5_651.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/28\/5\/651\/48881557\/bioinformatics_28_5_651.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T15:30:14Z","timestamp":1674660614000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/28\/5\/651\/248490"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,1,12]]},"references-count":20,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2012,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bts027","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2012,3,1]]},"published":{"date-parts":[[2012,1,12]]}}}