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NPInter v5.0: ncRNA interaction database in a new era.
Zheng, Yu; Luo, Huaxia; Teng, Xueyi; Hao, Xinpei; Yan, Xiaoyu; Tang, Yiheng; Zhang, Wanyu; Wang, Yuanxin; Zhang, Peng; Li, Yanyan; Zhao, Yi; Chen, Runsheng; He, Shunmin.
  • Zheng Y; Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
  • Luo H; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
  • Teng X; Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
  • Hao X; Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
  • Yan X; Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
  • Tang Y; University of Chinese Academy of Sciences, Beijing 100049, China.
  • Zhang W; Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
  • Wang Y; University of Chinese Academy of Sciences, Beijing 100049, China.
  • Zhang P; Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
  • Li Y; Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
  • Zhao Y; Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
  • Chen R; University of Chinese Academy of Sciences, Beijing 100049, China.
  • He S; Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
Nucleic Acids Res ; 2022 Nov 14.
Article in English | MEDLINE | ID: covidwho-2237602
ABSTRACT
Noncoding RNAs (ncRNAs) play key regulatory roles in biological processes by interacting with other biomolecules. With the development of high-throughput sequencing and experimental technologies, extensive ncRNA interactions have been accumulated. Therefore, we updated the NPInter database to a fifth version to document these interactions. ncRNA interaction entries were doubled from 1 100 618 to 2 596 695 by manual literature mining and high-throughput data processing. We integrated global RNA-DNA interactions from iMARGI, ChAR-seq and GRID-seq, greatly expanding the number of RNA-DNA interactions (from 888 915 to 8 329 382). In addition, we collected different types of RNA interaction between SARS-CoV-2 virus and its host from recently published studies. Long noncoding RNA (lncRNA) expression specificity in different cell types from tumor single cell RNA-seq (scRNA-seq) data were also integrated to provide a cell-type level view of interactions. A new module named RBP was built to display the interactions of RNA-binding proteins with annotations of localization, binding domains and functions. In conclusion, NPInter v5.0 (http//bigdata.ibp.ac.cn/npinter5/) provides informative and valuable ncRNA interactions for biological researchers.

Full text: Available Collection: International databases Database: MEDLINE Language: English Year: 2022 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Language: English Year: 2022 Document Type: Article