Abstract
BackgroundThe GENCODE project has collected over 10,000 human long non-coding RNA (lncRNA) genes. However, the vast majority of them remain to be functionally characterized. Computational investigation of potential functions of human lncRNA genes is helpful to guide further experimental studies on lncRNAs.ResultsIn this study, based on expression correlation between lncRNAs and protein-coding genes across 19 human normal tissues, we used the hypergeometric test to functionally annotate a single lncRNA or a set of lncRNAs with significantly enriched functional terms among the protein-coding genes that are significantly co-expressed with the lncRNA(s). The functional terms include all nodes in the Gene Ontology (GO) and 4,380 human biological pathways collected from 12 pathway databases. We successfully mapped 9,625 human lncRNA genes to GO terms and biological pathways, and then developed the first ontology-driven user-friendly web interface named lncRNA2Function, which enables researchers to browse the lncRNAs associated with a specific functional term, the functional terms associated with a specific lncRNA, or to assign functional terms to a set of human lncRNA genes, such as a cluster of co-expressed lncRNAs. The lncRNA2Function is freely available at http://mlg.hit.edu.cn/lncrna2function.ConclusionsThe LncRNA2Function is an important resource for further investigating the functions of a single human lncRNA, or functionally annotating a set of human lncRNAs of interest.
Highlights
IntroductionThe GENCODE project has collected over 10,000 human long non-coding RNA (lncRNA) genes
The GENCODE project has collected over 10,000 human long non-coding RNA genes
Among the top ranked 200 Gene Ontology (GO) biological processes and pathways, we found that long non-coding RNA (lncRNA) play roles in many important biological processes, including defense response to bacterium, DNA packaging, meiosis, developmental process, metabolic process, cell cycle process, cell adhesion, cell differentiation, Jak-STAT signaling pathway and PI3K-Akt signaling pathway
Summary
The GENCODE project has collected over 10,000 human long non-coding RNA (lncRNA) genes. Computational investigation of potential functions of human lncRNA genes is helpful to guide further experimental studies on lncRNAs. Thousands of human long non-coding RNAs (lncRNAs) have been identified and emerging studies have revealed that lncRNAs play important roles in a wide range of biological processes [1,2] and diseases [3,4]. Functions of a lncRNA may be determined by loss- and gain-offunction biological experiments [5,6]. This is not straightforward since it is difficult to knock down a lncRNA expressed as multiple isoforms.
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