NPInter documents functional interactions between noncoding RNAs (except tRNAs and rRNAs) and biomolecules (proteins, RNAs and DNAs) which are experimentally verified. By functional interactions, we mean primarily physical interactions, although several interactions of other forms also appear here. Interactions are manually collected from publication in peer-reviewed journals, followed by an annotation process against known databases including NONCODE, miRBase and UniProt. We introduce a classification of the functional interaction data, which is based on the functional interaction process the ncRNA takes part in. NPInter also provides an efficient search option, allowing discovery of interactions, related publications and other information. NPInter is one of the 42 expert databases chosen by RNAcentral database.
We have become aware that the diversity of genes cannot approximate the diversity of functions within an organism, and systems biology is increasingly important for discovery of the new properties of biological systems. One major question is to understand how the various components of biological systems are combined to produce these new properties. However, to practice systems biology, one must capture global sets of combinational biological data such as protein-protein, protein-DNA and protein-RNA interactions.
NcRNAs are found in all analyzed organisms, and participates in numerous cellular processes. Novel ncRNAs and their functional interactions with other biomolecules are continuously being reported in the literature. Functional interaction experiments are, however, concentrated to the six major model species - Escherichia coli, Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Mus musculus and Homo sapiens. Over the recent years, several databases have been established to collect, organize and classify ncRNA sequences and information, such as Rfam, RNAdb, Noncoding RNAs database (at poznan) and NONCODE. Simultaneously KEGG, DIP,IntAct, BIND, MIPS and some other biomolecular interaction databases have been established, which primarily deal with the protein-protein interactions. Despite the growing number of databases, no database has been established to particularly collect ncRNA functional interaction data, and no bio-molecules network with an ncRNA component has been described. Therefore, we have so far not been able to easily search ncRNA functional interactions information in a user-friendly environment. And the noncoding RNAs become 'dark matter' in the bio-molecules network research.
(1). The amount of data in NPInter increases sharply. We newly added approximately 1.40 million interaction pairs into NPInter v5.0.
(2). We collected global RNA-DNA interactions. Datasets were from techniques including iMARGI, ChAR-seq and GRID-seq, and a total of 4.96 million RNA-DNA interaction pairs were added.
(3). A new module focused on RBP was added according to users’ feedback. 277 RBPs of human were listed in this module with three types of properties including function, localization and domain to filter specific RBPs.
(4). We specifically collected SARS-CoV-2 related RNA interactions. 1,567 SARS-CoV-2 related interactions including five panels were added.
(5). We viewed interactions of lncRNAs specifically expressed in cell types from scRNA-seq data. We collected scRNA-seq data from published literature to identify cell type specific lncRNAs in cancer, and presented interactions of existing lncRNAs in our database.