{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,26]],"date-time":"2026-01-26T11:38:21Z","timestamp":1769427501958,"version":"3.49.0"},"reference-count":52,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2022,10,27]],"date-time":"2022-10-27T00:00:00Z","timestamp":1666828800000},"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":["61772426"],"award-info":[{"award-number":["61772426"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["U1811262"],"award-info":[{"award-number":["U1811262"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,11,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Long non-coding RNAs (lncRNAs) can disrupt the biological functions of protein-coding genes (PCGs) to cause cancer. However, the relationship between lncRNAs and PCGs remains unclear and difficult to predict. Machine learning has achieved a satisfactory performance in association prediction, but to our knowledge, it is currently less used in lncRNA\u2013PCG association prediction. Therefore, we introduce GAE-LGA, a powerful deep learning model with graph autoencoders as components, to recognize potential lncRNA\u2013PCG associations. GAE-LGA jointly explored lncRNA\u2013PCG learning and cross-omics correlation learning for effective lncRNA\u2013PCG association identification. The functional similarity and multi-omics similarity of lncRNAs and PCGs were accumulated and encoded by graph autoencoders to extract feature representations of lncRNAs and PCGs, which were subsequently used for decoding to obtain candidate lncRNA\u2013PCG pairs. Comprehensive evaluation demonstrated that GAE-LGA can successfully capture lncRNA\u2013PCG associations with strong robustness and outperformed other machine learning-based identification methods. Furthermore, multi-omics features were shown to improve the performance of lncRNA\u2013PCG association identification. In conclusion, GAE-LGA can act as an efficient application for lncRNA\u2013PCG association prediction with the following advantages: It fuses multi-omics information into the similarity network, making the feature representation more accurate; it can predict lncRNA\u2013PCG associations for new lncRNAs and identify potential lncRNA\u2013PCG associations with high accuracy.<\/jats:p>","DOI":"10.1093\/bib\/bbac452","type":"journal-article","created":{"date-parts":[[2022,10,28]],"date-time":"2022-10-28T12:33:55Z","timestamp":1666960435000},"source":"Crossref","is-referenced-by-count":13,"title":["GAE-LGA: integration of multi-omics data with graph autoencoders to identify lncRNA\u2013PCG associations"],"prefix":"10.1093","volume":"23","author":[{"given":"Meihong","family":"Gao","sequence":"first","affiliation":[{"name":"School of Computer Science and Engineering, Northwestern Polytechnical University , Xi\u2019an 710072, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuhui","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Northwestern Polytechnical University , Xi\u2019an 710072, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yang","family":"Qi","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Northwestern Polytechnical University , Xi\u2019an 710072, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinpeng","family":"Guo","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Northwestern Polytechnical University , Xi\u2019an 710072, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xuequn","family":"Shang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Northwestern Polytechnical University , Xi\u2019an 710072, 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