title: IAOseq: inferring abundance of overlapping genes using RNA-seq data.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.forename: Hong
authors.initials: H
authors.lastname: Sun
authors.forename: Shuang
authors.initials: S
authors.lastname: Yang
authors.forename: Liangliang
authors.initials: L
authors.lastname: Tun
authors.forename: Yixue
authors.initials: Y
authors.lastname: Li
mesh_terms: D019295:Computational Biology / Q000379:methods*; D057225:Data Mining; D020869:Gene Expression Profiling; D015723:Gene Library; D005807:Genes, Overlapping / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic
chemical_list: D012333:RNA, Messenger