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RNA-seq 时间序列中差异异构体表达的鉴定和可视化。

Identification and visualization of differential isoform expression in RNA-seq time series.

机构信息

Mathematics Department, University of Alicante, Alicante 03690, Spain.

Genomics of Gene Expression Laboratory, Centro de Investigación Príncipe Felipe, Valencia 42012, Spain.

出版信息

Bioinformatics. 2018 Feb 1;34(3):524-526. doi: 10.1093/bioinformatics/btx578.

DOI:10.1093/bioinformatics/btx578
PMID:28968682
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5860359/
Abstract

MOTIVATION: As sequencing technologies improve their capacity to detect distinct transcripts of the same gene and to address complex experimental designs such as longitudinal studies, there is a need to develop statistical methods for the analysis of isoform expression changes in time series data. RESULTS: Iso-maSigPro is a new functionality of the R package maSigPro for transcriptomics time series data analysis. Iso-maSigPro identifies genes with a differential isoform usage across time. The package also includes new clustering and visualization functions that allow grouping of genes with similar expression patterns at the isoform level, as well as those genes with a shift in major expressed isoform. AVAILABILITY AND IMPLEMENTATION: The package is freely available under the LGPL license from the Bioconductor web site. CONTACT: mj.nueda@ua.es or aconesa@ufl.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

摘要

动机：随着测序技术提高了检测同一基因的不同转录本的能力，并能够处理纵向研究等复杂的实验设计，因此需要开发用于分析时间序列数据中异构体表达变化的统计方法。

结果：Iso-maSigPro 是 R 包 maSigPro 中用于转录组时间序列数据分析的新功能。Iso-maSigPro 可识别在不同时间具有不同异构体使用情况的基因。该软件包还包括新的聚类和可视化功能，允许在异构体水平上对具有相似表达模式的基因进行分组，以及对主要表达异构体发生变化的基因进行分组。

可用性和实现：该软件包可根据 LGPL 许可证在 Bioconductor 网站上免费获得。

联系方式：mj.nueda@ua.es 或 aconesa@ufl.edu。

补充信息：补充数据可在 Bioinformatics 在线获得。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b6e1/5860359/e3154c77c228/btx578f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b6e1/5860359/89079b0e91a3/btx578f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b6e1/5860359/e3154c77c228/btx578f2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b6e1/5860359/89079b0e91a3/btx578f1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/b6e1/5860359/e3154c77c228/btx578f2.jpg

相似文献

[1]
Identification and visualization of differential isoform expression in RNA-seq time series.

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[2]
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[3]
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[4]
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[5]
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[7]
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[9]
TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference.

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[10]
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[6]
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[8]
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本文引用的文献

[1]
Herboxidiene triggers splicing repression and abiotic stress responses in plants.

BMC Genomics. 2017-3-27

[2]
Statistical modeling of isoform splicing dynamics from RNA-seq time series data.

Bioinformatics. 2016-6-17

[3]
Analysis of differential splicing suggests different modes of short-term splicing regulation.

Bioinformatics. 2016-6-15

[4]
The neurogenetics of alternative splicing.

Nat Rev Neurosci. 2016-5

[5]
Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series.

Bioinformatics. 2014-9-15

[6]
Streaming fragment assignment for real-time analysis of sequencing experiments.

Nat Methods. 2012-11-18

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