NPInter

The noncoding RNAs and protein related biomacromolecules interaction database (NPInter; http://bioinfo.ibp.ac.cn/NPInter or http://www.bioinfo.org.cn/NPInter) is a database that documents experimentally determined functional interactions between noncoding RNAs (ncRNAs) and protein related biomacromolecules (PRMs) (proteins, mRNAs or genomic DNAs). NPInter intends to provide the scientific community with a comprehensive and integrated tool for efficient browsing and extraction of information on interactions between ncRNAs and PRMs. Beyond cataloguing details of these interactions, the NPInter will be useful for understanding ncRNA function, as it adds a very important functional element, ncRNAs, to the biomolecule interaction network and sets up a bridge between the coding and the noncoding kingdoms.[1]

NPInter (http://www.bioinfo.org/NPInter) is a database that integrates experimentally verified functional interactions between noncoding RNAs (excluding tRNAs and rRNAs) and other biomolecules (proteins, RNAs and genomic DNAs). Extensive studies on ncRNA interactions have shown that ncRNAs could act as part of enzymatic or structural complexes, gene regulators or other functional elements. With the development of high-throughput biotechnology, such as cross-linking immunoprecipitation and high-throughput sequencing (CLIP-seq), the number of known ncRNA interactions, especially those formed by protein binding, has grown rapidly in recent years. In this work, we updated NPInter to version 2.0 by collecting ncRNA interactions from recent literature and related databases, expanding the number of entries to 201 107 covering 18 species. In addition, NPInter v2.0 incorporated a service for the BLAST alignment search as well as visualization of interactions.[2]

Despite the fact that a large quantity of noncoding RNAs (ncRNAs) have been identified, their functions remain unclear. 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 tRNAs and rRNAs), especially long noncoding RNAs (lncRNAs) and other biomolecules (proteins, mRNAs, miRNAs and genomic DNAs). In NPInter v3.0, interactions pertaining to ncRNAs are not only manually curated from scientific literature but also curated from high-throughput technologies. In addition, we also curated lncRNA-miRNA interactions fromin silicopredictions supported by AGO CLIP-seq data. When compared with NPInter v2.0, the interactions are more informative (with additional information on tissues or cell lines, binding sites, conservation, co-expression values and other features) and more organized (with divisions on data sets by data sources, tissues or cell lines, experiments and other criteria). NPInter v3.0 expands the data set to 491,416 interactions in 188 tissues (or cell lines) from 68 kinds of experimental technologies. NPInter v3.0 also improves the user interface and adds new web services, including a local UCSC Genome Browser to visualize binding sites. Additionally, NPInter v3.0 defined a high-confidence set of interactions and predicted the functions of lncRNAs in human and mouse based on the interactions curated in the database. NPInter v3.0 is available athttp://www.bioinfo.org/NPInter/Database URL:http://www.bioinfo.org/NPInter/.[3]

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