TomExpress, a unified tomato RNA-Seq platform for visualization of expression data, clustering and correlation networks

The TomExpress platform was developed to provide the tomato research community with a browser and integrated web tools for public RNA-Seq data visualization and data mining. To avoid major biases that can result from the use of different mapping and statistical processing methods, RNA-Seq raw sequence data available in public databases were mapped de novo on a unique tomato reference genome sequence and post-processed using the same pipeline with accurate parameters. Following the calculation of the number of counts per gene in each RNA-Seq sample, a communal global normalization (标准化) method was applied to all expression values. This unifies the whole set of expression data and makes them comparable. A database was designed where each expression value is associated with corresponding experimental annotations. Sample details were manually curated to be easily understandable by biologists. To make the data easily searchable, a user-friendly web interface was developed that provides versatile (多功能的) data mining web tools via on-the-fly generation (动态生成) of output graphics, such as expression bar plots, comprehensive in planta representations and heatmaps of hierarchically (分等级地) clustered expression data. In addition, it allows for the identification of co-expressed genes and the visualization of correlation networks of co-regulated gene groups. TomExpress provides one of the most complete free resources of publicly available tomato RNA-Seq data, and allows for the immediate interrogation of transcriptional programs that regulate vegetative and reproductive development in tomato under diverse conditions. The design of the pipeline developed in this project enables easy updating of the database with newly published RNA-Seq data, thereby allowing for continuous enrichment of the resource.

作者构建了一个番茄转录组数据可视化和数据挖掘的网络平台TomExpress (http://tomexpress.toulouse.inra.fr)。

研究方向：番茄果实成形和果实发育中的生长素信号转导和表观遗传学。

doi: 10.1111/tpj.13711