Mayba Oleg, Gilbert Houston N, Liu Jinfeng, Haverty Peter M, Jhunjhunwala Suchit, Jiang Zhaoshi, Watanabe Colin, Zhang Zemin
Genome Biol. 2014 Aug 7;15(8):405. doi: 10.1186/s13059-014-0405-3.
Allele-specific gene expression, ASE, is an important aspect of gene regulation. We developed a novel method MBASED, meta-analysis based allele-specific expression detection for ASE detection using RNA-seq data that aggregates information across multiple single nucleotide variation loci to obtain a gene-level measure of ASE, even when prior phasing information is unavailable. MBASED is capable of one-sample and two-sample analyses and performs well in simulations. We applied MBASED to a panel of cancer cell lines and paired tumor-normal tissue samples, and observed extensive ASE in cancer, but not normal, samples, mainly driven by genomic copy number alterations.
等位基因特异性基因表达（ASE）是基因调控的一个重要方面。我们开发了一种新方法MBASED，即基于荟萃分析的等位基因特异性表达检测方法，用于利用RNA测序数据检测ASE。该方法通过汇总多个单核苷酸变异位点的信息，即使在没有先验定相信息的情况下，也能获得基因水平的ASE测量值。MBASED能够进行单样本和两样本分析，并且在模拟中表现良好。我们将MBASED应用于一组癌细胞系和配对的肿瘤-正常组织样本，观察到癌症样本（而非正常样本）中存在广泛的ASE，主要由基因组拷贝数改变驱动。
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