| Title | OncoBase: a platform for decoding regulatory somatic mutations in human cancers |
| Authors | Li, Xianfeng Shi, Leisheng Wang, Yan Zhong, Jianing Zhao, Xiaolu Teng, Huajing Shi, Xiaohui Yang, Haonan Ruan, Shasha Li, MingKun Sun, Zhong Sheng Zhan, Qimin Mao, Fengbiao |
| Affiliation | Peking Univ, Key Lab Carcinogenesis & Translat Res, Minist Educ Beijing, Lab Mol Oncol,Canc Hosp & Inst, Beijing 100142, Peoples R China Chinese Acad Sci, Beijing Inst Life Sci, Beijing 100101, Peoples R China Chinese Acad Sci, Key Lab Genom & Precis Med, Beijing Inst Genom, Beijing 100101, Peoples R China Gannan Med Univ, Key Lab Prevent & Treatment Cardiovasc & Cerebrov, Minist Educ, Ganzhou 341000, Peoples R China Univ Michigan, Dept Pathol, Ann Arbor, MI 48109 USA Univ Chinese Acad Sci, Sino Danish Coll, Beijing 100049, Peoples R China Wuhan Univ, Dept Clin Oncol, Renmin Hosp, Wuhan 430072, Hubei, Peoples R China |
| Issue Date | 2019 |
| Publisher | NUCLEIC ACIDS RESEARCH |
| Abstract | Whole-exome and whole-genome sequencing have revealed millions of somatic mutations associated with different human cancers, and the vast majority of them are located outside of coding sequences, making it challenging to directly interpret their functional effects. With the rapid advances in high-throughput sequencing technologies, genome-scale long-range chromatin interactions were detected, and distal target genes of regulatory elements were determined using three-dimensional (3D) chromatin looping. Herein, we present OncoBase (http://www.oncobase.biols.ac.cn/), an integrated database for annotating 81 385 242 somatic mutations in 68 cancer types from more than 120 cancer projects by exploring their roles in distal interactions between target genes and regulatory elements. OncoBase integrates local chromatin signatures, 3D chromatin interactions in different cell types and reconstruction of enhancer-target networks using state-of-the-art algorithms. It employs informative visualization tools to display the integrated local and 3D chromatin signatures and effects of somatic mutations on regulatory elements. Enhancer-promoter interactions estimated from chromatin interactions are integrated into a network diffusion system that quantitatively prioritizes somatic mutations and target genes from a large pool. Thus, OncoBase is a useful resource for the functional annotation of regulatory noncoding regions and systematically benchmarking the regulatory effects of embedded noncoding somatic mutations in human carcinogenesis. |
| URI | http://hdl.handle.net/20.500.11897/551542 |
| ISSN | 0305-1048 |
| DOI | 10.1093/nar/gky1139 |
| Indexed | SCI(E) |
| Appears in Collections: | 北京肿瘤医院 |
