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.
In NPInter v3.0, we have upgrades in several aspects:
1. 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 from in silico predictions supported by AGO CLIP-seq data.
2. The amount of data in NPInter increased sharply. The previous version of NPInter collected 201,107 interactions from 18 model organisms. NPInter v3.0, however, expanded the data set to 491,416 interactions in 188 tissues (or cell lines) from 68 kinds of experimental technologies.
3. In addition, we assigned NONCODE IDs, miRBase IDs, Ensembl IDs and RefSeq IDs to ncRNAs, instead of NONCODE IDs only.
4. NPInter v3.0 have also been improved the user interface and added new web services, including a local UCSC Genome Browser to visualize binding sites.
5. 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).
6. 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.
How to cite?NPInter v3.0 IS Online!.
|RNA-RNA||152,521||High-throughput data combined with LncPro prediction||96,244||Binding;Regulatory||134,725|
|DNA-TF||36||miRanda and TargetScan with Ago CLIP data||33,366||Expression correlation||65|
|DNA-DNA||9||miRanda with Ago CLIP data||39,447||Coexpression||54|
|DNA-Protein||2||TargetScan with Ago CLIP data||61,912|