Laboratory of Translational Genomics - Centre for Integrative Biology, University of Trento, Via delle Regole 101, 38123 Mattarello (TN) and Institute of Biophysics CNR - Via alla Cascata 56/C, 38123 Povo (TN), Italy.
Bioinformatics. 2014 Jan 15;30(2):289-91. doi: 10.1093/bioinformatics/btt634. Epub 2013 Nov 12.
High-throughput technologies have led to an explosion of genomic data available for automated analysis. The consequent possibility to simultaneously sample multiple layers of variation along the gene expression flow requires computational methods integrating raw information from different '-omics'. It has been recently demonstrated that translational control is a widespread phenomenon, with profound and still underestimated regulation capabilities. Although detecting changes in the levels of total messenger RNAs (mRNAs; the transcriptome), of polysomally loaded mRNAs (the translatome) and of proteins (the proteome) is experimentally feasible in a high-throughput way, the integration of these levels is still far from being robustly approached. Here we introduce tRanslatome, a new R/Bioconductor package, which is a complete platform for the simultaneous pairwise analysis of transcriptome, translatome and proteome data. The package includes most of the available statistical methods developed for the analysis of high-throughput data, allowing the parallel comparison of differentially expressed genes and the corresponding differentially enriched biological themes. Notably, it also enables the prediction of translational regulatory elements on mRNA sequences. The utility of this tool is demonstrated with two case studies.
tRanslatome is available in Bioconductor.
高通量技术已经导致大量可供自动分析的基因组数据。随之而来的可能性是沿着基因表达流同时采样多个变异层，这需要将来自不同“组学”的原始信息整合在一起的计算方法。最近已经证明，翻译控制是一种普遍现象，具有深远且仍被低估的调节能力。尽管以高通量的方式在实验上可以检测总信使 RNA（mRNA；转录组）、多聚核糖体加载的 mRNAs（翻译组）和蛋白质（蛋白质组）水平的变化，但这些水平的整合远未得到稳健的研究。在这里，我们引入了 tRanslatome，这是一个新的 R/Bioconductor 包，它是同时分析转录组、翻译组和蛋白质组数据的完整平台。该软件包包含了大多数为分析高通量数据开发的统计方法，允许对差异表达基因和相应的差异富集的生物学主题进行并行比较。值得注意的是，它还能够预测 mRNA 序列上的翻译调控元件。该工具的实用性通过两个案例研究得到了证明。
tRanslatome 可在 Bioconductor 中获得。
