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NPInter v5.0: ncRNA interaction database in a new era

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 fift...

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Detalles Bibliográficos
Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825547/
https://www.ncbi.nlm.nih.gov/pubmed/36373614
http://dx.doi.org/10.1093/nar/gkac1002
Descripción
Sumario: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.