Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis

被引：145
|
作者：
Finotello, Francesca [1 ]
Di Camillo, Barbara [2 ]
机构：
[1] Univ Padua, Dept Informat Engn, I-35131 Padua, Italy
[2] Univ Padua, Dept Informat Engn, Bioengn, I-35131 Padua, Italy
来源：
BRIEFINGS IN FUNCTIONAL GENOMICS | 2015年 / 14卷 / 02期
关键词：
RNA-seq; differential gene expression; NGS; next-generation sequencing; transcriptomics; ALIGNMENT ALGORITHMS; STATISTICAL-METHODS; READ ALIGNMENT; LENGTH BIAS; QUANTIFICATION; NORMALIZATION; IDENTIFICATION; TOOLS; DNA; TRANSCRIPTOMES;
D O I：
10.1093/bfgp/elu035
中图分类号：
Q81 [生物工程学（生物技术）]; Q93 [微生物学];
学科分类号：
071005 ; 0836 ; 090102 ; 100705 ;
摘要：
RNA-seq is a methodology for RNA profiling based on next-generation sequencing that enables to measure and compare gene expression patterns at unprecedented resolution. Although the appealing features of this technique have promoted its application to a wide panel of transcriptomics studies, the fast-evolving nature of experimental protocols and computational tools challenges the definition of a unified RNA-seq analysis pipeline. In this review, focused on the study of differential gene expression with RNA-seq, we go through themain steps of data processing and discuss open challenges and possible solutions.
引用
收藏
页码：130 / 142
页数：13
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