title: ncFANs: a web server for functional annotation of long non-coding RNAs.
abstract: Recent interest in the non-coding transcriptome has resulted in the identification of large numbers of long non-coding RNAs (lncRNAs) in mammalian genomes, most of which have not been functionally characterized. Computational exploration of the potential functions of these lncRNAs will therefore facilitate further work in this field of research. We have developed a practical and user-friendly web interface called ncFANs (non-coding RNA Function ANnotation server), which is the first web service for functional annotation of human and mouse lncRNAs. On the basis of the re-annotated Affymetrix microarray data, ncFANs provides two alternative strategies for lncRNA functional annotation: one utilizing three aspects of a coding-non-coding gene co-expression (CNC) network, the other identifying condition-related differentially expressed lncRNAs. ncFANs introduces a highly efficient way of re-using the abundant pre-existing microarray data. The present version of ncFANs includes re-annotated CDF files for 10 human and mouse Affymetrix microarrays, and the server will be continuously updated with more re-annotated microarray platforms and lncRNA data. ncFANs is freely accessible at http://www.ebiomed.org/ncFANs/ or http://www.noncode.org/ncFANs/.
authors.affiliation: Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, PR China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Liao
authors.forename: Hui
authors.initials: H
authors.lastname: Xiao
authors.forename: Dechao
authors.initials: D
authors.lastname: Bu
authors.forename: Chaoyong
authors.initials: C
authors.lastname: Xie
authors.forename: Ruoyu
authors.initials: R
authors.lastname: Miao
authors.forename: Haitao
authors.initials: H
authors.lastname: Luo
authors.forename: Guoguang
authors.initials: G
authors.lastname: Zhao
authors.forename: Kuntao
authors.initials: K
authors.lastname: Yu
authors.forename: Haitao
authors.initials: H
authors.lastname: Zhao
authors.forename: Geir
authors.initials: G
authors.lastname: Skogerbø
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
authors.forename: Zhongdao
authors.initials: Z
authors.lastname: Wu
authors.forename: Changning
authors.initials: C
authors.lastname: Liu
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhao
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling; D006801:Humans; D020407:Internet; D051379:Mice; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis; D022661:RNA, Untranslated / Q000378:metabolism*; D012984:Software; D014584:User-Computer Interface
chemical_list: D022661:RNA, Untranslated