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. The amount of data in NPInter increases sharply. The previous version of NPInter released contain 201,107 interactions from 18 model organisms. NPInter v3.0, however, contains 915,067 interactions of ncRNA with other biomolecules from 22 organisms.
2. In addition, we add tissue and cell type infromation of interactions and give ncRNAs accession IDs from Ensemble and RefSeq.
3. By integrating the local UCSC Genome Browser, NPInter v3.0 visualizes binding site locations in human, mouse and yeast.
4. Tools are added to NPInter v3.0 to predict RNA-RNA and RNA-protein interactions.
How to cite?NPInter v2.0 : Nucleic Acids Res. 2013 Nov 11.NPInter : Nucleic Acids Res. 2006 Jan 1.
| Level | Num | Class | Num | Binding Sites | Num |
|---|---|---|---|---|---|
| RNA-Protein | 186,433 | Regulatory | 720,034 | Homo sapiens | 1,396,686 |
| RNA-RNA | 724,765 | Binding | 194,914 | Mus musculus | 73,523 |
| RNA-DNA | 3,822 | Coexpression | 54 | Saccharomyces cerevisiae | 1,314 |
| DNA-TF | 36 | Expression Correlation | 65 | ||
| DNA-DNA | 9 | ||||
| DNA-Protein | 2 |