DELongSeq for efficient detection of differential isoform expression from long-read RNA-seq data.
DELongSeq for efficient detection of differential isoform expression from long-read RNA-seq data.
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DOI：
10.1093/nargab/lqad019
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发表时间：
2023-03
影响因子：
4.6
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传统的基因表达定量方法，如微阵列或定量PCR，对所有基因的估计具有相似的变化。然而，下一代短读段或长读段测序使用读段计数来估计具有宽得多的动态范围的表达水平。除了估计的异构体表达的准确性外，衡量估计不确定性程度的效率也是下游分析的重要因素。我们提出了DELongSeq算法，它采用EM算法的信息矩阵来量化异构体表达估计的不确定性，以提高估计效率。DELongSeq使用随机效应回归模型分析DE亚型，因为研究内变异代表亚型表达估计的可变精密度，研究间变异代表样本间亚型表达水平的变异。更重要的是，DELongSeq允许1个病例对1个对照的差异表达比较，这在精准医学中有特定的应用场景（比如治疗前对治疗后，或者肿瘤对基质组织）。通过对几个RNA-Seq数据集的广泛模拟和分析，我们表明不确定性量化方法在计算上是可靠的，并且可以提高异构体或基因的差异表达（DE）分析的能力。总之，DELongSeq允许从长读段RNA-Seq数据中有效检测差异同种型/基因表达。
Conventional gene expression quantification approaches, such as microarrays or quantitative PCR, have similar variations of estimates for all genes. However, next-generation short-read or long-read sequencing use read counts to estimate expression levels with much wider dynamic ranges. In addition to the accuracy of estimated isoform expression, efficiency, which measures the degree of estimation uncertainty, is also an important factor for downstream analysis. Instead of read count, we present DELongSeq, which employs information matrix of EM algorithm to quantify uncertainty of isoform expression estimates to improve estimation efficiency. DELongSeq uses random-effect regression model for the analysis of DE isoform, in that within-study variation represents variable precision in isoform expression estimation and between-study variation represents variation in isoform expression levels across samples. More importantly, DELongSeq allows 1 case versus 1 control comparison of differential expression, which has specific application scenarios in precision medicine (such as before versus after treatment, or tumor versus stromal tissues). Through extensive simulations and analysis of several RNA-Seq datasets, we show that the uncertainty quantification approach is computationally reliable, and can improve the power of differential expression (DE) analysis of isoforms or genes. In summary, DELongSeq allows for efficient detection of differential isoform/gene expression from long-read RNA-Seq data.