蛋白质基因组学
鸟枪蛋白质组学
蛋白质组学
RNA序列
计算生物学
生物
蛋白质组
核糖核酸
选择性拼接
定量蛋白质组学
转录组
RNA剪接
基因
信使核糖核酸
生物信息学
基因表达
遗传学
作者
Xiaojing Wang,Qi Liu,Bing Zhang
出处
期刊:Proteomics
[Wiley]
日期:2014-11-17
卷期号:14 (23-24): 2676-2687
被引量:68
标识
DOI:10.1002/pmic.201400184
摘要
RNA sequencing (RNA‐Seq) and MS‐based shotgun proteomics are powerful high‐throughput technologies for identifying and quantifying RNA transcripts and proteins, respectively. With the increasing affordability of these technologies, many projects have started to apply both to the same samples to achieve a more comprehensive understanding of biological systems. A major analytical challenge for such integrative projects is how to effectively leverage the complementary nature of RNA‐Seq and shotgun proteomics data. RNA‐Seq provides comprehensive information on mRNA abundance, alternative splicing, nucleotide variation, and structure alteration. Sample‐specific protein databases derived from RNA‐Seq data can better approximate the real protein pools in cell and tissue samples and thus improve protein identification. Meanwhile, proteomics data provide essential confirmation of the validity and functional relevance of novel findings from RNA‐Seq data. At the quantitative level, mRNA and protein levels are only modestly correlated, suggesting strong involvement of posttranscriptional regulation in controlling gene expression. Here, we review recent studies at the interface of RNA‐Seq and proteomics data. We discuss goals, accomplishments, and challenges in RNA‐Seq‐based proteogenomics. We also examine the current status and future potential of parallel transcriptome and proteome quantification in revealing posttranscriptional regulatory mechanisms.
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