Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads

BMC Genomics

Research

Yufei Huang¹  Devanand Sarkar²  Zhao Lai³  Yi Zou³  Yuanhang Liu⁴  Hung-I Harry Chen⁵  Yidong Chen⁶ 

[1] Department of Electrical and Computer Engineering, The University of Texas at San Antonio, 78249, San Antonio, TX, USA;Departments of Human and Molecular Genetics, Virginia Commonwealth University, 23284, Richmond, VA, USA;VCU Institute of Molecular Medicine (VIMM), Virginia Commonwealth University, 23284, Richmond, VA, USA;Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, 78229, San Antonio, TX, USA;Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, 78229, San Antonio, TX, USA;Department of Cellular and Structural Biology, The University of Texas Health Science Center at San Antonio, 78229, San Antonio, TX, USA;Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, 78229, San Antonio, TX, USA;Department of Electrical and Computer Engineering, The University of Texas at San Antonio, 78249, San Antonio, TX, USA;Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, 78229, San Antonio, TX, USA;Department of Epidemiology & Biostatistics, The University of Texas Health Science Center at San Antonio, 78229, San Antonio, TX, USA;

关键词: RNA-Seq;    Differential expression analysis;    XBSeq;    DESeq;    Non-exonic mapped reads;    Negative binomial distribution;    Poisson distribution;   

DOI  :  10.1186/1471-2164-16-S7-S14

来源: Springer

【 摘 要 】

BackgroundRNA sequencing (RNA-seq) is a powerful tool for genome-wide expression profiling of biological samples with the advantage of high-throughput and high resolution. There are many existing algorithms nowadays for quantifying expression levels and detecting differential gene expression, but none of them takes the misaligned reads that are mapped to non-exonic regions into account. We developed a novel algorithm, XBSeq, where a statistical model was established based on the assumption that observed signals are the convolution of true expression signals and sequencing noises. The mapped reads in non-exonic regions are considered as sequencing noises, which follows a Poisson distribution. Given measureable observed and noise signals from RNA-seq data, true expression signals, assuming governed by the negative binomial distribution, can be delineated and thus the accurate detection of differential expressed genes.ResultsWe implemented our novel XBSeq algorithm and evaluated it by using a set of simulated expression datasets under different conditions, using a combination of negative binomial and Poisson distributions with parameters derived from real RNA-seq data. We compared the performance of our method with other commonly used differential expression analysis algorithms. We also evaluated the changes in true and false positive rates with variations in biological replicates, differential fold changes, and expression levels in non-exonic regions. We also tested the algorithm on a set of real RNA-seq data where the common and different detection results from different algorithms were reported.ConclusionsIn this paper, we proposed a novel XBSeq, a differential expression analysis algorithm for RNA-seq data that takes non-exonic mapped reads into consideration. When background noise is at baseline level, the performance of XBSeq and DESeq are mostly equivalent. However, our method surpasses DESeq and other algorithms with the increase of non-exonic mapped reads. Only in very low read count condition XBSeq had a slightly higher false discovery rate, which may be improved by adjusting the background noise effect in this situation. Taken together, by considering non-exonic mapped reads, XBSeq can provide accurate expression measurement and thus detect differential expressed genes even in noisy conditions.

【 授权许可】

CC BY   
© Chen et al.; licensee BioMed Central Ltd. 2015