Defining essentiality score of protein-coding genes and long noncoding RNAs

Abstract

Measuring the essentiality of genes is critically important in biology and medicine. Here we proposed a computational method, GIC (Gene Importance Calculator), which can efficiently predict the essentiality of both protein-coding genes and long noncoding RNAs (lncRNAs) based on only sequence information. For identifying the essentiality of protein-coding genes, GIC outperformed well-established computational scores. In an independent mouse lncRNA dataset, GIC also achieved an exciting performance (AUC = 0.918). In contrast, the traditional computational methods are not applicable to lncRNAs. Moreover, we explored several potential applications of GIC score. Firstly, we revealed a correlation between gene GIC score and research hotspots of genes. Moreover, GIC score can be used to evaluate whether a gene in mouse is representative for its homolog in human by dissecting its cross-species difference. This is critical for basic medicine because many basic medical studies are performed in animal models. Finally, we showed that GIC score can be used to identify candidate genes from a transcriptomics study. GIC is freely available at http://www.cuilab.cn/gic/.