title: MetaRNA-Seq: An Interactive Tool to Browse and Annotate Metadata from RNA-Seq Studies.
abstract: 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.
authors.affiliation: Weill Cornell Medical College in Qatar, Education City, Doha, Qatar.
authors.forename: Pankaj
authors.initials: P
authors.lastname: Kumar
authors.affiliation: Weill Cornell Medical College in Qatar, Education City, Doha, Qatar.
authors.forename: Anna
authors.initials: A
authors.lastname: Halama
authors.affiliation: Weill Cornell Medical College in Qatar, Education City, Doha, Qatar.
authors.forename: Shahina
authors.initials: S
authors.lastname: Hayat
authors.affiliation: Weill Cornell Medical College in Qatar, Education City, Doha, Qatar.
authors.forename: Anja M
authors.initials: AM
authors.lastname: Billing
authors.affiliation: Weill Cornell Medical College in Qatar, Education City, Doha, Qatar.
authors.forename: Manish
authors.initials: M
authors.lastname: Gupta
authors.affiliation: Weill Cornell Medical College in Qatar, Education City, Doha, Qatar.
authors.forename: Noha A
authors.initials: NA
authors.lastname: Yousri
authors.affiliation: Weill Cornell Medical College in Qatar, Education City, Doha, Qatar.
authors.forename: Gregory M
authors.initials: GM
authors.lastname: Smith
authors.affiliation: Weill Cornell Medical College in Qatar, Education City, Doha, Qatar ; Institute of Bioinformatics and System Biology, Helmholtz Zentrum Munchen, Germany Research Center of Environmental Health, 85764 Neuherberg, Germany.
authors.forename: Karsten
authors.initials: K
authors.lastname: Suhre
mesh_terms: D019295:Computational Biology; D030541:Databases, Genetic; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D058977:Molecular Sequence Annotation / Q000379:methods*; D012313:RNA / Q000032:analysis* / Q000145:classification*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
chemical_list: D012313:RNA