title: Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks.
abstract: More and more evidences demonstrate that the long non-coding RNAs (lncRNAs) play many key roles in diverse biological processes. There is a critical need to annotate the functions of increasing available lncRNAs. In this article, we try to apply a global network-based strategy to tackle this issue for the first time. We develop a bi-colored network based global function predictor, long non-coding RNA global function predictor ('lnc-GFP'), to predict probable functions for lncRNAs at large scale by integrating gene expression data and protein interaction data. The performance of lnc-GFP is evaluated on protein-coding and lncRNA genes. Cross-validation tests on protein-coding genes with known function annotations indicate that our method can achieve a precision up to 95%, with a suitable parameter setting. Among the 1713 lncRNAs in the bi-colored network, the 1625 (94.9%) lncRNAs in the maximum connected component are all functionally characterized. For the lncRNAs expressed in mouse embryo stem cells and neuronal cells, the inferred putative functions by our method highly match those in the known literature.
authors.affiliation: School of computer science and technology, Xidian University, 2 South Taibai Road, Xi'an Shaanxi, 710071, PR China.
authors.forename: Xingli
authors.initials: X
authors.lastname: Guo
authors.forename: Lin
authors.initials: L
authors.lastname: Gao
authors.forename: Qi
authors.initials: Q
authors.lastname: Liao
authors.forename: Hui
authors.initials: H
authors.lastname: Xiao
authors.forename: Xiaoke
authors.initials: X
authors.lastname: Ma
authors.forename: Xiaofei
authors.initials: X
authors.lastname: Yang
authors.forename: Haitao
authors.initials: H
authors.lastname: Luo
authors.forename: Guoguang
authors.initials: G
authors.lastname: Zhao
authors.forename: Dechao
authors.initials: D
authors.lastname: Bu
authors.forename: Fei
authors.initials: F
authors.lastname: Jiao
authors.forename: Qixiang
authors.initials: Q
authors.lastname: Shao
authors.forename: RunSheng
authors.initials: R
authors.lastname: Chen
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhao
mesh_terms: D000465:Algorithms; D000818:Animals; D001921:Brain / Q000378:metabolism; D053595:Embryonic Stem Cells / Q000378:metabolism; D015870:Gene Expression; D006801:Humans; D051379:Mice; D058977:Molecular Sequence Annotation / Q000379:methods*; D009474:Neurons / Q000378:metabolism; D060066:Protein Interaction Maps; D062085:RNA, Long Noncoding / Q000378:metabolism / Q000502:physiology*
chemical_list: D062085:RNA, Long Noncoding