RNA-Seq 数据中全基因组差异剪接的软件研究综述。
A survey of software for genome-wide discovery of differential splicing in RNA-Seq data.
机构信息
Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, 12801 17th Ave, rm 12103, MS 8108, PO Box 6511, Aurora, CO 80045, USA.
出版信息
Hum Genomics. 2014 Jan 21;8(1):3. doi: 10.1186/1479-7364-8-3.
Abstract
Alternative splicing is a major contributor to cellular diversity. Therefore the identification and quantification of differentially spliced transcripts in genome-wide transcript analysis is an important consideration. Here, I review the software available for analysis of RNA-Seq data for differential splicing and discuss intrinsic challenges for differential splicing analyses. Three approaches to differential splicing analysis are described, along with their associated software implementations, their strengths, limitations, and caveats. Suggestions for future work include more extensive experimental validation to assess accuracy of the software predictions and consensus formats for outputs that would facilitate visualizations, data exchange, and downstream analyses.
摘要
可变剪接是细胞多样性的主要贡献者。因此，在全基因组转录分析中鉴定和定量差异剪接的转录本是一个重要的考虑因素。在这里，我回顾了用于 RNA-Seq 数据差异剪接分析的软件，并讨论了差异剪接分析的内在挑战。描述了三种差异剪接分析方法，以及它们各自的软件实现、优点、局限性和注意事项。对未来工作的建议包括更广泛的实验验证，以评估软件预测的准确性，以及输出的共识格式，这将有助于可视化、数据交换和下游分析。
相似文献
1
A survey of software for genome-wide discovery of differential splicing in RNA-Seq data.RNA-Seq 数据中全基因组差异剪接的软件研究综述。
Hum Genomics. 2014 Jan 21;8(1):3. doi: 10.1186/1479-7364-8-3.
2
A survey of best practices for RNA-seq data analysis.RNA测序数据分析的最佳实践调查。
Genome Biol. 2016 Jan 26;17:13. doi: 10.1186/s13059-016-0881-8.
3
A survey of computational methods in transcriptome-wide alternative splicing analysis.转录组范围可变剪接分析中的计算方法综述。
Biomol Concepts. 2015 Mar;6(1):59-66. doi: 10.1515/bmc-2014-0040.
4
Gene expression and splicing alterations analyzed by high throughput RNA sequencing of chronic lymphocytic leukemia specimens.通过慢性淋巴细胞白血病标本的高通量RNA测序分析基因表达和剪接改变。
BMC Cancer. 2015 Oct 16;15:714. doi: 10.1186/s12885-015-1708-9.
5
Alternative Splicing Signatures in RNA-seq Data: Percent Spliced in (PSI).RNA测序数据中的可变剪接特征：剪接百分率（PSI）
Curr Protoc Hum Genet. 2015 Oct 6;87:11.16.1-11.16.14. doi: 10.1002/0471142905.hg1116s87.
6
SplicingCompass: differential splicing detection using RNA-seq data.SplicingCompass：使用 RNA-seq 数据进行差异剪接检测。
Bioinformatics. 2013 May 1;29(9):1141-8. doi: 10.1093/bioinformatics/btt101. Epub 2013 Feb 28.
7
Detection and quantification of alternative splicing variants using RNA-seq.使用RNA测序技术检测和定量可变剪接变体
Methods Mol Biol. 2012;883:97-110. doi: 10.1007/978-1-61779-839-9_7.
8
AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana.AtRTD——一个用于准确量化拟南芥转录本特异性表达的全面参考转录本数据集资源。
New Phytol. 2015 Oct;208(1):96-101. doi: 10.1111/nph.13545. Epub 2015 Jun 25.
9
Design of RNA splicing analysis null models for post hoc filtering of Drosophila head RNA-Seq data with the splicing analysis kit (Spanki).利用剪接分析试剂盒（Spanki）对果蝇头部 RNA-Seq 数据进行事后过滤的 RNA 剪接分析零模型设计。
BMC Bioinformatics. 2013 Nov 9;14:320. doi: 10.1186/1471-2105-14-320.
10
Read-Split-Run: an improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data.读取-分割-运行：一种利用RNA测序数据识别全基因组非经典剪接区域的改进型生物信息学流程。
BMC Genomics. 2016 Aug 22;17 Suppl 7(Suppl 7):503. doi: 10.1186/s12864-016-2896-7.
引用本文的文献
1
Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of mutations.慢性淋巴细胞白血病和骨髓增生异常综合征患者的长读转录组测序揭示了突变的分子效应。
Genome Res. 2024 Nov 20;34(11):1832-1848. doi: 10.1101/gr.279327.124.
2
Differential splicing of neuronal genes in a Trem2*R47H mouse model mimics alterations associated with Alzheimer's disease.神经元基因在 Trem2*R47H 小鼠模型中的差异剪接模拟了与阿尔茨海默病相关的改变。
BMC Genomics. 2023 Apr 4;24(1):172. doi: 10.1186/s12864-023-09280-x.
3
Insights into Transcriptomic Differences in Ovaries between Lambs and Adult Sheep after Superovulation Treatment.超数排卵处理后羔羊与成年绵羊卵巢转录组差异的研究洞察
Animals (Basel). 2023 Feb 14;13(4):665. doi: 10.3390/ani13040665.
4
Alternative RNA splicing in stem cells and cancer stem cells: Importance of transcript-based expression analysis.干细胞和癌症干细胞中的可变RNA剪接：基于转录本的表达分析的重要性。
World J Stem Cells. 2021 Oct 26;13(10):1394-1416. doi: 10.4252/wjsc.v13.i10.1394.
5
Maternal methionine supplementation during gestation alters alternative splicing and DNA methylation in bovine skeletal muscle.妊娠期间母体蛋氨酸补充改变了牛骨骼肌中的选择性剪接和 DNA 甲基化。
BMC Genomics. 2021 Oct 30;22(1):780. doi: 10.1186/s12864-021-08065-4.
6
Altered splicing associated with the pathology of inflammatory bowel disease.与炎症性肠病病理相关的剪接改变。
Hum Genomics. 2021 Jul 23;15(1):47. doi: 10.1186/s40246-021-00347-y.
7
Genome-wide discovery of natural variation in pre-mRNA splicing and prioritising causal alternative splicing to salt stress response in rice.水稻前体mRNA剪接自然变异的全基因组发现及盐胁迫响应中因果性可变剪接的优先级确定
New Phytol. 2021 May;230(3):1273-1287. doi: 10.1111/nph.17189. Epub 2021 Feb 14.
8
Revised Exon Structure of l-DOPA Decarboxylase () Reveals Novel Splice Variants Associated with Colorectal Cancer Progression.l-DOPA 脱羧酶 () 外显子结构的修订揭示了与结直肠癌进展相关的新型剪接变体。
Int J Mol Sci. 2020 Nov 13;21(22):8568. doi: 10.3390/ijms21228568.
9
Alternative splicing is highly variable among Daphnia pulex lineages in response to acute copper exposure.轮虫铜暴露急性反应中，多态种间可变剪接差异显著。
BMC Genomics. 2020 Jun 26;21(1):433. doi: 10.1186/s12864-020-06831-4.
10
Systematic evaluation of differential splicing tools for RNA-seq studies.基于 RNA-seq 研究的差异剪接工具的系统评估
Brief Bioinform. 2020 Dec 1;21(6):2052-2065. doi: 10.1093/bib/bbz126.
本文引用的文献
1
Genomics: the state of the art in RNA-seq analysis.基因组学：RNA测序分析的最新技术水平
Nat Methods. 2013 Dec;10(12):1165-6. doi: 10.1038/nmeth.2735.
2
Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors.达成目的之手段：信使核糖核酸前体的可变聚腺苷酸化机制
Wiley Interdiscip Rev RNA. 2014 Mar-Apr;5(2):183-96. doi: 10.1002/wrna.1206. Epub 2013 Nov 14.
3
Assessment of transcript reconstruction methods for RNA-seq.RNA-seq 转录本重构方法评估。
Nat Methods. 2013 Dec;10(12):1177-84. doi: 10.1038/nmeth.2714. Epub 2013 Nov 3.
4
Global splicing pattern reversion during somatic cell reprogramming.体细胞重编程过程中的全局剪接模式逆转
Cell Rep. 2013 Oct 31;5(2):357-66. doi: 10.1016/j.celrep.2013.09.016. Epub 2013 Oct 17.
5
GLiMMPS: robust statistical model for regulatory variation of alternative splicing using RNA-seq data.GLiMMPS：使用 RNA-seq 数据进行剪接调控变异的稳健统计模型。
Genome Biol. 2013 Jul 22;14(7):R74. doi: 10.1186/gb-2013-14-7-r74.
6
Evaluating the impact of sequencing depth on transcriptome profiling in human adipose.评估测序深度对人体脂肪转录组分析的影响。
PLoS One. 2013 Jun 24;8(6):e66883. doi: 10.1371/journal.pone.0066883. Print 2013.
7
SplicingCompass: differential splicing detection using RNA-seq data.SplicingCompass：使用 RNA-seq 数据进行差异剪接检测。
Bioinformatics. 2013 May 1;29(9):1141-8. doi: 10.1093/bioinformatics/btt101. Epub 2013 Feb 28.
8
Alternative splicing: a pivotal step between eukaryotic transcription and translation.可变剪接：真核转录与翻译之间的关键步骤。
Nat Rev Mol Cell Biol. 2013 Mar;14(3):153-65. doi: 10.1038/nrm3525. Epub 2013 Feb 6.
9
Identifying differentially spliced genes from two groups of RNA-seq samples.从两组 RNA-seq 样本中鉴定差异剪接基因。
Gene. 2013 Apr 10;518(1):164-70. doi: 10.1016/j.gene.2012.11.045. Epub 2012 Dec 8.
10
Differential analysis of gene regulation at transcript resolution with RNA-seq.基于 RNA-seq 的转录分辨率下基因调控的差异分析。
Nat Biotechnol. 2013 Jan;31(1):46-53. doi: 10.1038/nbt.2450. Epub 2012 Dec 9.
Zotero 插件