{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,10]],"date-time":"2026-02-10T17:05:29Z","timestamp":1770743129639,"version":"3.49.0"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2024,9,3]],"date-time":"2024-09-03T00:00:00Z","timestamp":1725321600000},"content-version":"vor","delay-in-days":40,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Distinguished and Excellent Young Scholars Cultivation Project of Shanxi Agricultural University","award":["2022YQPYGC09"],"award-info":[{"award-number":["2022YQPYGC09"]}]},{"name":"Fundamental Research Program of Shanxi Province","award":["202303021211098"],"award-info":[{"award-number":["202303021211098"]}]},{"name":"Fundamental Research Program of Shanxi Province","award":["20210302124129"],"award-info":[{"award-number":["20210302124129"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Fund of China","doi-asserted-by":"crossref","award":["82274363"],"award-info":[{"award-number":["82274363"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,7,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Systematic characterization of biological effects to genetic perturbation is essential to the application of molecular biology and biomedicine. However, the experimental exhaustion of genetic perturbations on the genome-wide scale is challenging. Here, we show TranscriptionNet, a deep learning model that integrates multiple biological networks to systematically predict transcriptional profiles to three types of genetic perturbations based on transcriptional profiles induced by genetic perturbations in the L1000 project: RNA interference, clustered regularly interspaced short palindromic repeat, and overexpression. TranscriptionNet performs better than existing approaches in predicting inducible gene expression changes for all three types of genetic perturbations. TranscriptionNet can predict transcriptional profiles for all genes in existing biological networks and increases perturbational gene expression changes for each type of genetic perturbation from a few thousand to 26\u00a0945 genes. TranscriptionNet demonstrates strong generalization ability when comparing predicted and true gene expression changes on different external tasks. Overall, TranscriptionNet can systemically predict transcriptional consequences induced by perturbing genes on a genome-wide scale and thus holds promise to systemically detect gene function and enhance drug development and target discovery.<\/jats:p>","DOI":"10.1093\/bib\/bbae433","type":"journal-article","created":{"date-parts":[[2024,9,3]],"date-time":"2024-09-03T14:18:23Z","timestamp":1725373103000},"source":"Crossref","is-referenced-by-count":5,"title":["A genome-scale deep learning model to predict gene expression changes of genetic perturbations from multiplex biological networks"],"prefix":"10.1093","volume":"25","author":[{"given":"Lingmin","family":"Zhan","sequence":"first","affiliation":[{"name":"College of Basic Sciences, Shanxi Agricultural University , 1 Mingxian South Road, Taigu District, Jinzhong, 030801 , China"}]},{"given":"Yingdong","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Basic Sciences, Shanxi Agricultural University , 1 Mingxian South Road, Taigu District, Jinzhong, 030801 , China"}]},{"given":"Aoyi","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Basic Sciences, Shanxi Agricultural University , 1 Mingxian South Road, Taigu District, Jinzhong, 030801 , China"}]},{"given":"Yuanyuan","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Basic Sciences, Shanxi Agricultural University , 1 Mingxian South Road, Taigu District, Jinzhong, 030801 , China"}]},{"given":"Caiping","family":"Cheng","sequence":"additional","affiliation":[{"name":"College of Basic Sciences, Shanxi Agricultural University , 1 Mingxian South Road, Taigu District, Jinzhong, 030801 , China"}]},{"given":"Jinzhong","family":"Zhao","sequence":"additional","affiliation":[{"name":"College of Basic Sciences, Shanxi Agricultural University , 1 Mingxian South Road, Taigu District, Jinzhong, 030801 , China"}]},{"given":"Wuxia","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Basic Sciences, Shanxi Agricultural University , 1 Mingxian South Road, Taigu District, Jinzhong, 030801 , China"}]},{"given":"Jianxin","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Traditional Chinese Medicine, Beijing University of Chinese Medicine , 11 North Third Ring Road East, Chaoyang District, Beijing 100029 , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8858-8106","authenticated-orcid":false,"given":"Peng","family":"Li","sequence":"additional","affiliation":[{"name":"College of Basic Sciences, Shanxi Agricultural University , 1 Mingxian South Road, Taigu District, Jinzhong, 030801 , China"}]}],"member":"286","published-online":{"date-parts":[[2024,9,3]]},"reference":[{"key":"2024090314180235500_ref1","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1038\/s41586-023-06490-x","article-title":"The status of the human gene 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