MetaRNA-Seq – An Interactive Tool to Browse and Annotate Metadata from RNA-Seq Studies

The number of RNA-Seq studies has grown in recent years. The design of RNA-Seq studies varies from very simple (e.g., two-condition case-control) to very complicated (e.g., time series involving multiple samples at each time point with separate drug treatments). Most of these publically available RNA-Seq studies are deposited in NCBI databases, but their metadata are scattered throughout four different databases: Sequence Read Archive (SRA), Biosample, Bioprojects, and Gene Expression Omnibus (GEO). Although the NCBI web interface is able to provide all of the metadata information, it often requires significant effort to retrieve study- or project-level information by traversing through multiple hyperlinks and going to another page. Moreover, project- and study-level metadata lack manual or automatic curation by categories, such as disease type, time series, case-control, or replicate type, which are vital to comprehending any RNA-Seq study.

Here, researchers from the Weill Cornell Medical College in Qatar introduce a new tool called “MetaRNA-Seq” to interactively browse, search, and annotate RNA-Seq metadata at the study level. MetaRNA-Seq provides an easy to use web interface to understand metadata for RNA-Seq studies. Most of the details about any RNA-Seq study are provided in the same window with a single click. MetaRNA-Seq provides a consensus summary for any RNA-Seq study by digesting all biosample, experiment, and run information for that study. In addition, MetaRNA-Seq provides the hierarchical data of the study in a tree-like structure. In MetaRNA-Seq, the metadata for a RNA-Seq study can be annotated and searched based on annotated fields, such as disease type, time series, case-control, replicate type, and customized annotation.

The MetaRNA-Seq web interface. On the left it has the search functionality for RNA-Seq studies. Below the search, the table contains all RNA-Seq study details, including name, title, number of samples, number of experiments, and number of runs, allowing one to quickly scroll through all of the studies. The table is filtered based on the search. The table can be sorted by double clicking any column. Upon clicking any study in the table, the study details are populated at the upper right. A tree-like data structure containing biosamples, experiments, and runs for the selected study is populated in the lower right.

Availability – MetaRNA-Seq is available at http://metarnaseqdb.screensifter.com/.