Abstract
Long non-coding RNAs (lncRNAs) are emerging as key regulators of diverse biological processes and diseases. However, the combinatorial effects of these molecules in a specific biological function are poorly understood. Identifying co-expressed protein-coding genes of lncRNAs would provide ample insight into lncRNA functions. To facilitate such an effort, we have developed Co-LncRNA, which is a web-based computational tool that allows users to identify GO annotations and KEGG pathways that may be affected by co-expressed protein-coding genes of a single or multiple lncRNAs. LncRNA co-expressed protein-coding genes were first identified in publicly available human RNA-Seq datasets, including 241 datasets across 6560 total individuals representing 28 tissue types/cell lines. Then, the lncRNA combinatorial effects in a given GO annotations or KEGG pathways are taken into account by the simultaneous analysis of multiple lncRNAs in user-selected individual or multiple datasets, which is realized by enrichment analysis. In addition, this software provides a graphical overview of pathways that are modulated by lncRNAs, as well as a specific tool to display the relevant networks between lncRNAs and their co-expressed protein-coding genes. Co-LncRNA also supports users in uploading their own lncRNA and protein-coding gene expression profiles to investigate the lncRNA combinatorial effects. It will be continuously updated with more human RNA-Seq datasets on an annual basis. Taken together, Co-LncRNA provides a web-based application for investigating lncRNA combinatorial effects, which could shed light on their biological roles and could be a valuable resource for this community.Database URL: http://www.bio-bigdata.com/Co-LncRNA/
Highlights
Large numbers of long non-coding RNAs with little or no protein-coding potential have been identified in mammalian genomes [1,2,3]
Co-LncRNA was designed to investigate the long non-coding RNAs (lncRNAs) combinatorial effects in the GO annotations and KEGG pathways based on human RNA-Seq data, and is available at http://www.bio-bigdata.com/Co-LncRNA/
In the current version of Co-LncRNA, the gene names could be represented by Ensembl gene ID or symbol, and two different types of methods were used to detect the co-expression pairs
Summary
Large numbers of long non-coding RNAs (lncRNAs) with little or no protein-coding potential have been identified in mammalian genomes [1,2,3]. LncRNAs are known to be involved in many important biological processes, including imprinting control, cell differentiation and development, and human complex diseases [6,7,8]. Most lncRNAs have not been functionally characterized, and their combinatorial effects are not known with respect to a specific biological function. Only 280 lncRNAs have been included in this database to date. Increasing evidence shows that lncRNAs can interact with DNA, RNA, protein molecules and/or in combinations, acting as essential regulators [10, 11]. Based on the hypothesis that lncRNA target genes are differentially expressed after lncRNA knockdown or overexpression, LncRNA2Target was developed, and a limited number of human lncRNAs were included [15]
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