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. 2014 Jan;42(Database issue):D104-8.
doi: 10.1093/nar/gkt1057. Epub 2013 Nov 11.

NPInter v2.0: an updated database of ncRNA interactions

Jiao Yuan  1 , Wei Wu, Chaoyong Xie, Guoguang Zhao, Yi Zhao, Runsheng Chen
Affiliations

NPInter v2.0: an updated database of ncRNA interactions

Jiao Yuan et al. Nucleic Acids Res. 2014 Jan.

Abstract

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.

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Figures

Figure 1.
Figure 1.
Overview of the NPInter v2.0 Database. NcRNA interactions were obtained from literature and specialized databases. RNA binding sites of individual proteins identified using genome-wide techniques were screened against NONCODE and only those correspond to NONCODE RNAs were extracted.
Figure 2.
Figure 2.
Graph visualization of NPInter interactions. Node colour and size indicates molecule type, while edge colour indicates interaction source. The initial placement of the nodes is determined by a ‘force-directed’ layout algorithm that aims to keep the more similar nodes closer together, but the placement may later be adjusted by the user.
See this image and copyright information in PMC

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