Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study.
Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study.
复制标题
DOI：
10.1186/1471-2105-13-331
复制
发表时间：
2012-12-13
影响因子：
3
通讯作者：
Liu H
中科院分区：
文献类型：
--
作者：
Sun L;Zhang Z;Bailey TL;Perkins AC;Tallack MR;Xu Z;Liu H
高通量RNA测序技术（RNA-Seq）的出现促进了对长链非编码RNA（lncRNA）的研究。然而，从RNA-Seq数据中识别lncRNA仍然不是微不足道的，并且揭示它们的功能仍然是一个挑战。我们提出了一个计算管道，用于从RNA-Seq数据中检测新的lncRNA。首先，基因组引导的转录组重建用于生成初始组装的转录物。根据定量表达水平过滤可能的部分转录物和伪影。之后，通过使用新开发的称为lncRScan的程序进一步过滤已知转录本和具有高蛋白质编码潜力的转录本来检测新的lncRNA。我们将我们的管道应用于小鼠Klf 1敲除数据集，并讨论了我们通过差异表达分析检测到的新型lncRNA的可能功能。我们鉴定了308个新的lncRNA候选者，与已知的蛋白质编码转录本相比，它们具有更短的转录本长度，更少的外显子，更短的推定开放阅读框架。在lncRNA中，52个大的基因间ncRNA（lincRNA）显示出比蛋白质编码的lncRNA更低的表达水平，并且13个lncRNA代表野生型和Klf 1敲除条件之间的显著差异表达。我们的方法可以从RNA-Seq数据预测一组新的lncRNA。其中一些lncRNA在野生型和Klf 1基因敲除菌株间的表达存在差异，提示这些新的lncRNA在进一步的功能研究中具有较高的优先性。
Study on long non-coding RNAs (lncRNAs) has been promoted by high-throughput RNA sequencing (RNA-Seq). However, it is still not trivial to identify lncRNAs from the RNA-Seq data and it remains a challenge to uncover their functions. We present a computational pipeline for detecting novel lncRNAs from the RNA-Seq data. First, the genome-guided transcriptome reconstruction is used to generate initially assembled transcripts. The possible partial transcripts and artefacts are filtered according to the quantified expression level. After that, novel lncRNAs are detected by further filtering known transcripts and those with high protein coding potential, using a newly developed program called lncRScan. We applied our pipeline to a mouse Klf1 knockout dataset, and discussed the plausible functions of the novel lncRNAs we detected by differential expression analysis. We identified 308 novel lncRNA candidates, which have shorter transcript length, fewer exons, shorter putative open reading frame, compared with known protein-coding transcripts. Of the lncRNAs, 52 large intergenic ncRNAs (lincRNAs) show lower expression level than the protein-coding ones and 13 lncRNAs represent significant differential expression between the wild-type and Klf1 knockout conditions. Our method can predict a set of novel lncRNAs from the RNA-Seq data. Some of the lncRNAs are showed differentially expressed between the wild-type and Klf1 knockout strains, suggested that those novel lncRNAs can be given high priority in further functional studies.
登录
查看更多内容
影响因子：
56.9
作者：
Carninci, P;Kasukawa, T;Hayashizaki, Y
通讯作者：
Hayashizaki, Y
影响因子：
3.7
作者：
Mitra SA;Mitra AP;Triche TJ
通讯作者：
Triche TJ
影响因子：
4.3
作者：
Dinger ME;Pang KC;Mercer TR;Mattick JS
通讯作者：
Mattick JS
DOI：
10.1093/bioinformatics/btr209
发表时间：
2011-07-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Lin MF;Jungreis I;Kellis M
通讯作者：
Kellis M
影响因子：
14.9
作者：
Hubbard, T;Barker, D;Clamp, M
通讯作者：
Clamp, M