RPASE: individual based allele-specific expression detection without prior knowledge of haplotype phase

Variation in gene expression is believed to make a significant contribution to phenotypic diversity and divergence. The analysis of allele-specific expression (ASE) can reveal important insights into gene expression regulation. We developed a novel method called RPASE (Read-backed Phasing-based ASE detection) to test for genes that show ASE. With mapped RNA-seq data from a single individual and a list of SNPs from the same individual as the only input, RPASE is capable of aggregating information across multiple dependent SNPs and producing individual-based gene-level tests for ASE. RPASE performs well in simulations and comparisons. We applied RPASE to multiple bird species and found a potentially rich landscape of ASE.基因表达变异被认为对表型多样性与分化具有重要贡献。等位基因特异性表达（allele-specific expression, ASE）分析可为基因表达调控机制提供重要见解。我们开发了一种名为RPASE（基于读段定相的等位基因特异性表达检测，Read-backed Phasing-based ASE detection）的全新方法，用于筛查表现出ASE现象的基因。该方法仅以单个个体的比对RNA测序（RNA-seq）数据与同一来源的单核苷酸多态性（single nucleotide polymorphisms, SNPs）列表作为唯一输入，能够整合多个相互关联的SNPs的信息，并生成基于个体的基因水平ASE检测结果。RPASE在模拟实验与对照比对中表现优异。我们将该方法应用于多个鸟类物种，发现了蕴含丰富ASE现象的潜在调控图谱。