Identifying compound-protein interactions with knowledge graph embedding of perturbation transcriptomics
文献类型：期刊论文
| 作者 | Ni, Shengkun1,2; Kong, Xiangtai1,2; Zhang, Yingying1,3,4; Chen, Zhengyang1,2; Wang, Zhaokun1,2; Fu, Zunyun1; Huo, Ruifeng1,5; Tong, Xiaochu1,2; Qu, Ning1,2; Wu, Xiaolong1,6 |
| 刊名 | CELL GENOMICS
 |
| 出版日期 | 2024-10-09 |
| 卷号 | 4期号:10页码:100655 |
| DOI | 10.1016/j.xgen.2024.100655 |
| 文献子类 | Article |
| 英文摘要 | The emergence of perturbation transcriptomics provides a new perspective for drug discovery, but existing analysis methods suffer from inadequate performance and limited applicability. In this work, we present PertKGE, a method designed to deconvolute compound-protein interactions from perturbation transcriptomics with knowledge graph embedding. By considering multi-level regulatory events within biological systems that share the same semantic context, PertKGE significantly improves deconvoluting accuracy in two critical cold-startsettings: inferring targets for new compounds and conducting virtual screening for new targets. We further demonstrate the pivotal role of incorporating multi-level regulatory events in alleviating representational biases. Notably, it enables the identification of ectonucleotide pyrophosphatase/ phosphodiesterase-1 as the target responsible for the unique anti-tumor immunotherapy effect of tankyrase inhibitor K-756 and the discovery of five novel hits targeting the emerging cancer therapeutic target aldehyde dehydrogenase 1B1 with a remarkable hit rate of 10.2%. These findings highlight the potential of PertKGE to accelerate drug discovery. |
| WOS关键词 | GENE-EXPRESSION ; CONNECTIVITY MAP ; DESCRIPTORS ; ASSAY ; V2.0 |
| WOS研究方向 | Cell Biology ; Genetics & Heredity |
| 语种 | 英语 |
| WOS记录号 | WOS:001333216200001 |
| 出版者 | ELSEVIER |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/317010]  |
| 专题 | 新药研究国家重点实验室 |
| 通讯作者 | Li, Xutong; Zhang, Sulin; Zheng, Mingyue |
| 作者单位 | 1.Chinese Acad Sci, Shanghai Inst Mat Med, Drug Discovery & Design Ctr, State Key Lab Drug Res, 555 Zuchongzhi Rd, Shanghai 201203, Peoples R China 2.Univ Chinese Acad Sci, 19A Yuquan Rd, Beijing 100049, Peoples R China 3.Univ Sci & Technol China, Sch Life Sci, Div Life Sci & Med, Hefei 230026, Peoples R China 4.Univ Sci & Technol China, Affiliated Hosp USTC 1, Anhui Prov Hosp, Div Life Sci & Med, Hefei 230001, Peoples R China 5.Nanjing Univ Chinese Med, 138 Xianlin Rd, Nanjing 210023, Peoples R China 6.East China Univ Sci & Technol, Sch Pharm, Shanghai 200237, Peoples R China 7.Univ Chinese Acad Sci, Hangzhou Inst Adv Study, Sch Pharmaceut Sci & Technol, Hangzhou 310024, Peoples R China |
| 推荐引用方式 GB/T 7714 | Ni, Shengkun,Kong, Xiangtai,Zhang, Yingying,et al. Identifying compound-protein interactions with knowledge graph embedding of perturbation transcriptomics[J]. CELL GENOMICS,2024,4(10):100655. |
| APA | Ni, Shengkun.,Kong, Xiangtai.,Zhang, Yingying.,Chen, Zhengyang.,Wang, Zhaokun.,...&Zheng, Mingyue.(2024).Identifying compound-protein interactions with knowledge graph embedding of perturbation transcriptomics.CELL GENOMICS,4(10),100655. |
| MLA | Ni, Shengkun,et al."Identifying compound-protein interactions with knowledge graph embedding of perturbation transcriptomics".CELL GENOMICS 4.10(2024):100655. |
入库方式： OAI收割
来源：上海药物研究所
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