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NPInter v4.0: an integrated database of ncRNA interactions

2019 Nucleic Acids Research  
We have therefore updated NPInter to its fourth edition in which are integrated 600 000 new experimentally identified ncRNA interactions. ncRNA-DNA interactions derived from ChIRP-seq data and circular  ...  To document regulatory interactions between ncRNAs and biomolecules, we previously created the NPInter database (http://bigdata.ibp.ac.cn/npinter).  ...  ACKNOWLEDGEMENTS Data analysis and computing resources were supported by the Center for Big Data Research in Health (http://bigdata. ibp.ac.cn), Institute of Biophysics, Chinese Academy of Sciences.  ... 
doi:10.1093/nar/gkz969 pmid:31670377 pmcid:PMC7145607 fatcat:s6onvm4movfglfhdc2emhxnuii

NPInter v3.0: an upgraded database of noncoding RNA-associated interactions

Yajing Hao, Wei Wu, Hui Li, Jiao Yuan, Jianjun Luo, Yi Zhao, Runsheng Chen
2016 Database: The Journal of Biological Databases and Curation  
NPInter v3.0: an upgraded database of noncoding RNA-associated interactions.  ...  To enable researchers to have a better understanding of ncRNAs' functions, we updated the NPInter database to version 3.0, which contains experimentally verified interactions between ncRNAs (excluding  ...  We also thank Dr Guifeng Wei and Dr Greg Vatcher for carefully reading of our article. Conflict of interest. None declared.  ... 
doi:10.1093/database/baw057 pmid:27087310 pmcid:PMC4834207 fatcat:3qn2qxign5h6bmofqxiuwixpji

RNAInter v4.0: RNA interactome repository with redefined confidence scoring system and improved accessibility

Juanjuan Kang, Qiang Tang, Jun He, Le Li, Nianling Yang, Shuiyan Yu, Mengyao Wang, Yuchen Zhang, Jiahao Lin, Tianyu Cui, Yongfei Hu, Puwen Tan (+6 others)
2021 Nucleic Acids Research  
iii) an update of entries to >47 million by manually mining the literature and integrating six database resources with evidence from experimental and computational sources.  ...  community and the types of tissues/cells, (ii) a redesigned fully functional database that enables for a more rapid retrieval and browsing of interactions via an upgraded user-friendly interface and (  ...  In addition, RNAInter integrated three experimentally validated databases LncTarD (11) , NPInter v4.0 (12) and NoncoRNA (13) as well as three computational predicted databases miRDB v6.0 (14) , oRNAment  ... 
doi:10.1093/nar/gkab997 pmid:34718726 pmcid:PMC8728132 fatcat:mfjljdehkje3fe5mmg6rkzs5ju

Bioinformatic Tools for the Analysis and Prediction of ncRNA Interactions

Andrés Rincón-Riveros, Duvan Morales, Josefa Antonia Rodríguez, Victoria E. Villegas, Liliana López-Kleine
2021 International Journal of Molecular Sciences  
This review describes the latest advances in databases, bioinformatic tools, and new in silico strategies that allow the establishment or prediction of biological interactions of ncRNAs, particularly miRNAs  ...  this knowledge by suggesting possible novel interactions of these ncRNAs with other molecules.  ...  • NPInter v4.0 NPInter is a database that is already well known. In 2019, it launched a new update with over 600,000 curated interactions.  ... 
doi:10.3390/ijms222111397 pmid:34768830 pmcid:PMC8583695 fatcat:llvctlgk6fd3hke3nfdktefjsy

Non-Coding RNA Databases in Cardiovascular Research

Deepak Balamurali, Monika Stoll
2020 Non-Coding RNA  
Here, we provide a compendium of the current ncRNA databases relevant to cardiovascular research.  ...  facets of ncRNA research like basic and functional annotation, expressional profile, structural and molecular changes, and interaction with other biomolecules.  ...  NPInter v4.0 has seen the addition of interactions of circRNAs, interactions between lncRNAs and the genome and the integration of disease association with the interaction function.  ... 
doi:10.3390/ncrna6030035 pmid:32887511 pmcid:PMC7549374 fatcat:aazbd3qlargv3bfpeeqz4o6ee4

Interaction and cross-talk between non-coding RNAs

Soichiro Yamamura, Mitsuho Imai-Sumida, Yuichiro Tanaka, Rajvir Dahiya
2017 Cellular and Molecular Life Sciences (CMLS)  
In this review, we will present and discuss these interactions, cross-talk, and co-regulation of ncRNAs and gene regulation due to these interactions.  ...  Interactions of miRNAs and lncRNAs have been reported to trigger decay of the targeted lncRNAs and have important roles in target gene regulation.  ...  Yuan J, Wu W, Xie C, Zhao G, Zhao Y et al (2014) NPInter v2.0: an updated database of ncRNA interactions. Nucleic Acids Res 42:D104-D108 63.  ... 
doi:10.1007/s00018-017-2626-6 pmid:28840253 pmcid:PMC5765200 fatcat:iswkollzw5aehckexpah6mspbu

NcPath: A novel tool for visualization and enrichment analysis of human non-coding RNA and KEGG signaling pathways [article]

Zutan Li, Yuanyuan Chen, Yuan Zhang, Jingya Fang, Zhihui Xu, Hao Zhang, Minfang Mao, Liangyun Zhang, Cong Pian
2022 bioRxiv   pre-print
Here, we redesigned a novel pathway database named NcPath by integrating and visualizing a total of 178,308 human experimentally-validated miRNA-target interactions (MTIs), 36,537 experimentally-verified  ...  To expand the application potential of the redesigned NcPath database, we identified 553,523 reliable lncRNA-PCG interaction pairs by integrating co-expression relations, ceRNA relations, co-TF-binding  ...  (vi) lncRNA-protein interactions identified by Clip-seq. We collected the human lncRNA-PCG interactions from the NPInter v4.0 database.  ... 
doi:10.1101/2022.06.03.494777 fatcat:bt44stwnt5dlri7bijuwdxe2lm

The Interplay between Long Noncoding RNAs and Proteins of the Epigenetic Machinery in Ovarian Cancer

Naiade Calanca, Cecilie Abildgaard, Cláudia Aparecida Rainho, Silvia Regina Rogatto
2020 Cancers  
We manually curated databases and used bioinformatics tools to identify lncRNAs implicated in the epigenetic regulation, along with examples of direct interactions between the lncRNAs and proteins of the  ...  Aberrant expression of lncRNAs is associated with epigenetic reprogramming during tumor development and progression, mainly due to their ability to interact with DNA, RNA, or proteins to regulate gene  ...  Integrates literature reported evidence and high-throughput data NPInter v4.0 processing to collect and illustrate functional http://bigdata.ibp.ac.cn/ npinter [118] interactions between ncRNAs and biomolecules  ... 
doi:10.3390/cancers12092701 pmid:32967233 pmcid:PMC7563210 fatcat:so7rj7275vb6fnlihwiejog6qq

Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review

Fotis A. Baltoumas, Sofia Zafeiropoulou, Evangelos Karatzas, Mikaela Koutrouli, Foteini Thanati, Kleanthi Voutsadaki, Maria Gkonta, Joana Hotova, Ioannis Kasionis, Pantelis Hatzis, Georgios A. Pavlopoulos
2021 Biomolecules  
Unfortunately, many of these databases are self-contained or poorly documented and maintained.  ...  To cope with this data flood, computational approaches, web services, and databases have been implemented to deal with issues such as data integration, visualization, exploration, organization, scalability  ...  The latest version of NPInter (v4.0) contains a total of 1100,658 interactions, composed by: (i) manually curated literature interactions, (ii) processed high-throughput sequencing data and (iii) interaction  ... 
doi:10.3390/biom11081245 pmid:34439912 pmcid:PMC8391349 fatcat:32aums2jtbc5vdcdknzfczajsy

Identification of cancer-related miRNA-lncRNA biomarkers using a basic miRNA-lncRNA network

Guangle Zhang, Cong Pian, Zhi Chen, Jin Zhang, Mingmin Xu, Liangyun Zhang, Yuanyuan Chen, Alfons Navarro
2018 PLoS ONE  
Thus, it is important to develop an effective method for the identification of cancer-related miRNA-lncRNA interactions.  ...  and lncRNAs in the TCGA (The Cancer Genome Atlas) database.  ...  Acknowledgments The authors would like to thank The Cancer Genome Atlas (TCGA) database for providing miRNA and lncRNA expression profiles of cancers, starBase v2.0, NPInter v3.0 and miRcode for providing  ... 
doi:10.1371/journal.pone.0196681 pmid:29715309 pmcid:PMC5929565 fatcat:yyi6mys43jhjvp67qnt4cbkjge

Fusing multiple protein-protein similarity networks to effectively predict lncRNA-protein interactions

Xiaoxiong Zheng, Yang Wang, Kai Tian, Jiaogen Zhou, Jihong Guan, Libo Luo, Shuigeng Zhou
2017 BMC Bioinformatics  
As lncRNA interacts with multiple proteins, predicting lncRNA-protein interactions (lncRPIs) is an important way to study the functions of lncRNA.  ...  Up to now, there have been a few works that exploit protein-protein interactions (PPIs) to help the prediction of new lncRPIs.  ...  Datasets We extracted Homo sapiens ncRNA-protein interactions from NPInter (v2.0) [17] and Homo sapiens lncRNA from the ncRNA database NONCODE (v4.0) [18] .  ... 
doi:10.1186/s12859-017-1819-1 pmid:29072138 pmcid:PMC5657051 fatcat:huxgbkc3dfdu7jmesduqnt5w5e

LPI-KTASLP: Prediction of lncRNA-Protein Interaction by Semi-Supervised Link Learning with Multivariate Information

Cong Shen, Yijie Ding, Jijun Tang, Limin Jiang, Fei Guo
2019 IEEE Access  
Our method of lncRNA-protein interaction prediction has been evaluated on a standard benchmark dataset of LPIs.  ...  interaction (LPI) identification.  ...  Homo sapiens lncRNA-protein interactions come from NPInter (v2.0), while protein sequences are obtained from the UniProt database and lncRNA database is NONCODE (v4.0).  ... 
doi:10.1109/access.2019.2894225 fatcat:irpw5jewjjfbfpdx3i3kd2bpem

Long noncoding RNAs: new insights in modulating mammalian spermatogenesis

Bahlibi Weldegebriall Sahlu, Shanjiang Zhao, Xiuge Wang, Saqib Umer, Huiying Zou, Jinming Huang, Huabin Zhu
2020 Journal of Animal Science and Biotechnology  
The expression of lncRNAs is biologically relevant in the highly dynamic and complex program of spermatogenesis and has become a research focus in recent genome studies.  ...  This multistage developmental process of spermatogenesis involves the expression of many male germ cell-specific long noncoding RNAs (lncRNAs) and highly regulated and specific gene expression.  ...  Acknowledgments The authors are grateful to the native English-speaking scientists of "Elixigen Company (Huntington Beach, California)" for proofreading the article.  ... 
doi:10.1186/s40104-019-0424-8 pmid:32128162 pmcid:PMC7047388 fatcat:3bmqgz5rsbfkpidwcxhhj6j5kq