Sun Hong, Yang Shuang, Tun Liangliang, Li Yixue
BMC Bioinformatics. 2015;16 Suppl 1(Suppl 1):S3. doi: 10.1186/1471-2105-16-S1-S3. Epub 2015 Jan 21.
Overlapping transcription constitutes a common mechanism for regulating gene expression. A major limitation of the overlapping transcription assays is the lack of high throughput expression data.
We developed a new tool (IAOseq) that is based on reads distributions along the transcribed regions to identify the expression levels of overlapping genes from standard RNA-seq data. Compared with five commonly used quantification methods, IAOseq showed better performance in the estimation accuracy of overlapping transcription levels. For the same strand overlapping transcription, currently existing high-throughput methods are rarely available to distinguish which strand was present in the original mRNA template. The IAOseq results showed that the commonly used methods gave an average of 1.6 fold overestimation of the expression levels of same strand overlapping genes.
This work provides a useful tool for mining overlapping transcription levels from standard RNA-seq libraries. IAOseq could be used to help us understand the complex regulatory mechanism mediated by overlapping transcripts. IAOseq is freely available at http://lifecenter.sgst.cn/main/en/IAO_seq.jsp.
重叠转录是调控基因表达的一种常见机制。重叠转录分析的一个主要局限是缺乏高通量表达数据。
我们开发了一种新工具（IAOseq），它基于转录区域的读段分布，从标准RNA测序数据中识别重叠基因的表达水平。与五种常用的定量方法相比，IAOseq在重叠转录水平的估计准确性方面表现更佳。对于同链重叠转录，目前现有的高通量方法很少能够区分原始mRNA模板中存在的是哪条链。IAOseq的结果表明，常用方法对同链重叠基因表达水平的估计平均高估了1.6倍。
这项工作为从标准RNA测序文库中挖掘重叠转录水平提供了一个有用的工具。IAOseq可用于帮助我们理解由重叠转录本介导的复杂调控机制。IAOseq可从http://lifecenter.sgst.cn/main/en/IAO_seq.jsp免费获取。
