Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq.
Detection and visualization of differential splicing in RNA-Seq data with JunctionSeq.
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DOI：
10.1093/nar/gkw501
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发表时间：
2016-09-06
影响因子：
14.9
通讯作者：
Mullikin JC
中科院分区：
文献类型：
--
作者：
Hartley SW;Mullikin JC
尽管RNA-Seq数据提供了前所未有的异构体水平表达信息，但替代异构体调节（AIR）的检测仍然很困难，特别是在使用不完整的转录本注释时。我们介绍JunctionSeq，这是一种新方法，它建立在成熟的DEXSeq软件包所使用的统计技术基础上，用于检测外显子区域和剪接点的差异使用。特别是，JunctionSeq能够检测新剪接点的差异使用，而不需要额外的同种型组装步骤，当可用的转录本注释有缺陷或不完整时，大大提高了性能。JunctionSeq还提供了一个强大而精简的可视化工具集，使生物信息学家能够快速直观地解释他们的结果。我们测试了我们的方法公开的数据，从几个实验中进行大鼠松果体和弓形虫，成功地检测已知的和以前验证的空气基因在19个基因水平的假设检验。由于其查询新剪接位点的能力，JunctionSeq仍然能够检测到这些差异，即使这些基因的所有替代同种型都不包括在转录本注释中。因此，JunctionSeq提供了一种强大的方法，用于检测替代同种型调节，即使是低质量的注释。JunctionSeq的实现可作为R/Bioconductor包提供。
Although RNA-Seq data provide unprecedented isoform-level expression information, detection of alternative isoform regulation (AIR) remains difficult, particularly when working with an incomplete transcript annotation. We introduce JunctionSeq, a new method that builds on the statistical techniques used by the well-established DEXSeq package to detect differential usage of both exonic regions and splice junctions. In particular, JunctionSeq is capable of detecting differential usage of novel splice junctions without the need for an additional isoform assembly step, greatly improving performance when the available transcript annotation is flawed or incomplete. JunctionSeq also provides a powerful and streamlined visualization toolset that allows bioinformaticians to quickly and intuitively interpret their results. We tested our method on publicly available data from several experiments performed on the rat pineal gland and Toxoplasma gondii, successfully detecting known and previously validated AIR genes in 19 out of 19 gene-level hypothesis tests. Due to its ability to query novel splice sites, JunctionSeq is still able to detect these differences even when all alternative isoforms for these genes were not included in the transcript annotation. JunctionSeq thus provides a powerful method for detecting alternative isoform regulation even with low-quality annotations. An implementation of JunctionSeq is available as an R/Bioconductor package.
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影响因子：
14.9
作者：
Hu Y;Huang Y;Du Y;Orellana CF;Singh D;Johnson AR;Monroy A;Kuan PF;Hammond SM;Makowski L;Randell SH;Chiang DY;Hayes DN;Jones C;Liu Y;Prins JF;Liu J
通讯作者：
Liu J
影响因子：
30.5
作者：
Bettigole SE;Lis R;Adoro S;Lee AH;Spencer LA;Weller PF;Glimcher LH
通讯作者：
Glimcher LH
影响因子：
48
作者：
Katz, Yarden;Wang, Eric T.;Airoldi, Edoardo M.;Burge, Christopher B.
通讯作者：
Burge, Christopher B.
影响因子：
48
作者：
Engstrom, Par G.;Steijger, Tamara;Sipos, Botond;Grant, Gregory R.;Kahles, Andre;Raetsch, Gunnar;Goldman, Nick;Hubbard, Tim J.;Harrow, Jennifer;Guigo, Roderic;Bertone, Paul
通讯作者：
Bertone, Paul
影响因子：
2.8
作者：
JIMENEZ, J;OSUNA, C;GUERRERO, JM
通讯作者：
GUERRERO, JM