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BioMed Research International
Volume 2015, Article ID 318064, 6 pages
Research Article

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

1Weill Cornell Medical College in Qatar, Education City, Doha, Qatar
2Institute of Bioinformatics and System Biology, Helmholtz Zentrum Munchen, Germany Research Center of Environmental Health, 85764 Neuherberg, Germany

Received 26 December 2014; Revised 10 April 2015; Accepted 11 April 2015

Academic Editor: Chih-Hsuan Wei

Copyright © 2015 Pankaj Kumar et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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 we describe “MetaRNA-Seq,” a new tool for interactively browsing, searching, and annotating RNA-Seq metadata with the capability of semiautomatic curation at the study level.