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Mass spectrometry\u2013based spatio-temporal proteomics technologies can help provide new insights of protein translocation, but bring the challenge in identifying reliable protein translocation events due to the noise interference and insufficient data mining. We propose a semi-supervised graph convolution network (GCN)\u2013based framework termed TransGCN that infers protein translocation events from spatio-temporal proteomics. Based on expanded multiple distance features and joint graph representations of proteins, TransGCN utilizes the semi-supervised GCN to enable effective knowledge transfer from proteins with known PSLs for predicting protein localization and translocation. Our results demonstrate that TransGCN outperforms current state-of-the-art methods in identifying protein translocations, especially in coping with batch effects. It also exhibited excellent predictive accuracy in PSL prediction. TransGCN is freely available on GitHub at https:\/\/github.com\/XuejiangGuo\/TransGCN.<\/jats:p>","DOI":"10.1093\/bib\/bbae055","type":"journal-article","created":{"date-parts":[[2024,3,1]],"date-time":"2024-03-01T09:44:58Z","timestamp":1709286298000},"source":"Crossref","is-referenced-by-count":3,"title":["TransGCN: a semi-supervised graph convolution network\u2013based framework to infer protein translocations in spatio-temporal proteomics"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0684-2789","authenticated-orcid":false,"given":"Bing","family":"Wang","sequence":"first","affiliation":[{"name":"Department of Histology and Embryology , State Key Laboratory of Reproductive Medicine and Offspring Health, , Nanjing 211166 , China"},{"name":"Nanjing Medical University , State Key Laboratory of Reproductive Medicine and Offspring Health, , Nanjing 211166 , China"},{"name":"School of Medicine, Southeast University , Nanjing 210009 , China"}]},{"given":"Xiangzheng","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Histology and Embryology , State Key Laboratory of Reproductive Medicine and Offspring Health, , Nanjing 211166 , China"},{"name":"Nanjing Medical University , State Key Laboratory of Reproductive Medicine and Offspring Health, , Nanjing 211166 , China"}]},{"given":"Xudong","family":"Han","sequence":"additional","affiliation":[{"name":"Department of Histology and Embryology , State Key Laboratory of Reproductive Medicine and Offspring Health, , Nanjing 211166 , China"},{"name":"Nanjing Medical University , State Key Laboratory of Reproductive Medicine and Offspring Health, , Nanjing 211166 , China"},{"name":"School of Medicine, Southeast University , Nanjing 210009 , China"}]},{"given":"Bingjie","family":"Hao","sequence":"additional","affiliation":[{"name":"Department of Histology and Embryology , State Key Laboratory of Reproductive Medicine and Offspring Health, , Nanjing 211166 , China"},{"name":"Nanjing Medical University , State Key Laboratory of Reproductive Medicine and Offspring Health, , Nanjing 211166 , China"}]},{"given":"Yan","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory , Sir Run Run Hospital, , Nanjing 211100 , China"},{"name":"Nanjing Medical University , Sir Run Run Hospital, , Nanjing 211100 , China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0475-5705","authenticated-orcid":false,"given":"Xuejiang","family":"Guo","sequence":"additional","affiliation":[{"name":"Department of Histology and Embryology , State Key Laboratory of Reproductive Medicine and Offspring Health, , Nanjing 211166 , China"},{"name":"Nanjing Medical University , State Key Laboratory of Reproductive Medicine and Offspring Health, , Nanjing 211166 , 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