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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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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
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author 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
author_facet 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
author_sort Zheng, Yu
collection PubMed
description 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.
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spelling pubmed-98255472023-01-10 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 Nucleic Acids Res Database Issue 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. Oxford University Press 2022-11-14 /pmc/articles/PMC9825547/ /pubmed/36373614 http://dx.doi.org/10.1093/nar/gkac1002 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Issue
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
NPInter v5.0: ncRNA interaction database in a new era
title NPInter v5.0: ncRNA interaction database in a new era
title_full NPInter v5.0: ncRNA interaction database in a new era
title_fullStr NPInter v5.0: ncRNA interaction database in a new era
title_full_unstemmed NPInter v5.0: ncRNA interaction database in a new era
title_short NPInter v5.0: ncRNA interaction database in a new era
title_sort npinter v5.0: ncrna interaction database in a new era
topic Database Issue
url 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
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