...
首页> 外文期刊>BMC Bioinformatics >Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study
【24h】

Prediction of novel long non-coding RNAs based on RNA-Seq data of mouse Klf1 knockout study

机译:基于小鼠Klf1基因敲除研究的RNA-Seq数据预测新型长非编码RNA

获取原文
   

获取外文期刊封面封底 >>

       

摘要

Background 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. Results 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. Conclusions 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.
机译:通过高通量RNA测序(RNA-Seq)促进了长非编码RNA(lncRNA)的背景研究。然而,从RNA-Seq数据中鉴定lncRNA仍然不是一件容易的事,要揭示其功能仍然是一个挑战。结果我们提出了一种用于从RNA-Seq数据中检测新型lncRNA的计算流水线。首先,基因组指导的转录组重建被用来生成最初组装的转录本。根据量化的表达水平过滤可能的部分转录本和假象。之后,使用新开发的名为lncRScan的程序,通过进一步过滤已知的转录本和具有高蛋白编码潜力的转录本,可以检测到新的lncRNA。我们将管道应用于小鼠Klf1基因敲除数据集,并讨论了通过差异表达分析检测到的新型lncRNA的合理功能。我们鉴定了308个新颖的lncRNA候选物,与已知的编码蛋白质的转录本相比,它们具有更短的转录长度,更少的外显子,更短的推定开放阅读框。在lncRNA中,有52个大型基因间ncRNA(lincRNA)的表达水平低于编码蛋白的表达水平,而13个lncRNA则在野生型和Klf1敲除条件之间表现出明显的差异表达。结论我们的方法可以从RNA-Seq数据中预测出一组新的lncRNA。一些lncRNAs在野生型和Klf1基因敲除菌株之间显示差异表达,这表明那些新的lncRNAs在进一步的功能研究中可以被赋予较高的优先级。

著录项

相似文献

  • 外文文献
  • 中文文献
  • 专利
获取原文

客服邮箱:kefu@zhangqiaokeyan.com

京公网安备:11010802029741号 ICP备案号:京ICP备15016152号-6 六维联合信息科技 (北京) 有限公司©版权所有
  • 客服微信

  • 服务号