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- Title
Comprehensive prediction of lncRNA–RNA interactions in human transcriptome.
- Authors
Terai, Goro; Iwakiri, Junichi; Kameda, Tomoshi; Hamada, Michiaki; Asai, Kiyoshi
- Abstract
Motivation: Recent studies have revealed that large numbers of non-coding RNAs are transcribed in humans, but only a few of them have been identified with their functions. Identification of the interaction target RNAs of the non-coding RNAs is an important step in predicting their functions. The current experimental methods to identify RNA–RNA interactions, however, are not fast enough to apply to a whole human transcriptome. Therefore, computational predictions of RNA–RNA interactions are desirable, but this is a challenging task due to the huge computational costs involved. Results: Here, we report comprehensive predictions of the interaction targets of lncRNAs in a whole human transcriptome for the first time. To achieve this, we developed an integrated pipeline for predicting RNA–RNA interactions on the K computer, which is one of the fastest super-computers in the world. Comparisons with experimentally-validated lncRNA–RNA interactions support the quality of the predictions. Additionally, we have developed a database that catalogs the predicted lncRNA–RNA interactions to provide fundamental information about the targets of lncRNAs.
- Subjects
RNA-RNA interactions; RNA sequencing; NON-coding RNA; TRANSCRIPTION factors; HUMAN genome
- Publication
BMC Genomics, 2016, Vol 17, p153
- ISSN
1471-2164
- Publication type
Article
- DOI
10.1186/s12864-015-2307-5