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Typically, hundreds or thousands of differentially expressed genes or proteins can be identified from omics data. This scale of possibilities is overwhelming for target discovery and validation using biochemical or cellular experiments. Most of these proteins and genes have no corresponding drugs or even active compounds. Moreover, a proportion of them may have been previously reported as being relevant to the disease of interest. To facilitate translational drug discovery from omics data, we have developed a new classification tool named Omics and Text driven Translational Medicine (OTTM). This tool can markedly narrow the range of proteins or genes that merit further validation via drug availability assessment and literature mining. For the 4489 candidate proteins identified in our previous proteomics study, OTTM recommended 40 FDA-approved or clinical trial drugs. Of these, 15 are available commercially and were tested on hepatocellular carcinoma Hep-G2 cells. Two drugs\u2014tafenoquine succinate (an FDA-approved antimalarial drug targeting CYC1) and branaplam (a Phase 3 clinical drug targeting SMN1 for the treatment of spinal muscular atrophy)\u2014showed potent inhibitory activity against Hep-G2 cell viability, suggesting that CYC1 and SMN1 may be potential therapeutic target proteins for hepatocellular carcinoma. In summary, OTTM is an efficient classification tool that can accelerate the discovery of effective drugs and targets using thousands of candidate proteins identified from omics data. The online and local versions of OTTM are available at http:\/\/otter-simm.com\/ottm.html.<\/jats:p>","DOI":"10.1093\/bib\/bbad301","type":"journal-article","created":{"date-parts":[[2023,8,18]],"date-time":"2023-08-18T14:22:19Z","timestamp":1692368539000},"source":"Crossref","is-referenced-by-count":5,"title":["OTTM: an automated classification tool for translational drug discovery from omics data"],"prefix":"10.1093","volume":"24","author":[{"given":"Xiaobo","family":"Yang","sequence":"first","affiliation":[{"name":"ShanghaiTech University"},{"name":"School of Life Science and Technology, ShanghaiTech University , 393 Huaxiazhong Road, Shanghai 200031 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bei","family":"Zhang","sequence":"additional","affiliation":[{"name":"Shanghai Institute of Materia Medica"},{"name":"Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, No.19A Yuquan Road, Beijing 100049 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siqi","family":"Wang","sequence":"additional","affiliation":[{"name":"Beijing Proteome Research Center"},{"name":"State Key Laboratory of Proteomics, Beijing Proteome Research Center, and National Center for Protein Sciences (Beijing)"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ye","family":"Lu","sequence":"additional","affiliation":[{"name":"Nanjing University of Chinese Medicine"},{"name":"School of Chinese Materia Medica, Nanjing University of Chinese Medicine , Nanjing 210023, China; Chemical Biology Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaixian","family":"Chen","sequence":"additional","affiliation":[{"name":"academician medicinal scientist of the Chinese Academy of 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