PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events.
PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events.
复制标题
DOI：
10.1186/s12859-016-0881-4
复制
发表时间：
2016-01-13
影响因子：
3
通讯作者：
Jackson MS
中科院分区：
文献类型：
--
作者：
Izuogu OG;Alhasan AA;Alafghani HM;Santibanez-Koref M;Elliott DJ;Jackson MS
已经经历转录后外显子改组（PTES）的转录物具有与基础基因组序列不一致的外显子顺序。这些已经在来自许多真核生物的各种组织和细胞类型中被鉴定，并且现在已知主要是环状的、细胞质的和非编码的。虽然没有统一的归属功能，有几个已被证明参与基因调控。然而，由于来自各种来源的人工制品，准确识别这些转录本可能很困难。在这里，我们提出了一种计算方法，PTESeq，从高通量RNAseq数据中识别这些转录本。独特的是，它系统地排除了来自假基因，片段重复和模板转换的潜在伪影，并输出PTES和典型外显子连接计数以便于比较分析。与现有的四种方法相比，PTESstrom在各种读取深度下实现了最高的特异性和相当的灵敏度。与最近用于鉴定人类环状RNA的公开方法相比，PTESstem还鉴定了13%至41.6%的结构。凭借高灵敏度和特异性，针对已知假阳性来源的用户可调过滤器，以及便于比较转录水平的定制输出，PTESTRA将有助于发现和分析这些知之甚少的转录本。本文的在线版本（doi：10.1186/s12859-016-0881-4）包含补充材料，可供授权用户使用。
Transcripts, which have been subject to Post-transcriptional exon shuffling (PTES), have an exon order inconsistent with the underlying genomic sequence. These have been identified in a wide variety of tissues and cell types from many eukaryotes, and are now known to be mostly circular, cytoplasmic, and non-coding. Although there is no uniformly ascribed function, several have been shown to be involved in gene regulation. Accurate identification of these transcripts can, however, be difficult due to artefacts from a wide variety of sources. Here, we present a computational method, PTESFinder, to identify these transcripts from high throughput RNAseq data. Uniquely, it systematically excludes potential artefacts emanating from pseudogenes, segmental duplications, and template switching, and outputs both PTES and canonical exon junction counts to facilitate comparative analyses. In comparison with four existing methods, PTESFinder achieves highest specificity and comparable sensitivity at a variety of read depths. PTESFinder also identifies between 13 % and 41.6 % more structures, compared to publicly available methods recently used to identify human circular RNAs. With high sensitivity and specificity, user-adjustable filters that target known sources of false positives, and tailored output to facilitate comparison of transcript levels, PTESFinder will facilitate the discovery and analysis of these poorly understood transcripts. The online version of this article (doi:10.1186/s12859-016-0881-4) contains supplementary material, which is available to authorized users.