MetaRNA-Seq

An interactive tool to browse and annotate metadata from RNA-Seq studies

Pankaj Kumar, Anna Halama, Shahina Hayat, Anja Billing, Manish Gupta, Noha Yousri, Gregory M. Smith, Karsten Suhre

Research output: Contribution to journalArticle

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.

Original languageEnglish
Article number318064
JournalBioMed Research International
Volume2015
DOIs
Publication statusPublished - 2015

Fingerprint

Metadata
RNA
Time series
Databases
Drug therapy
Gene expression
Gene Expression
Pharmaceutical Preparations

ASJC Scopus subject areas

  • Immunology and Microbiology(all)
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

MetaRNA-Seq : An interactive tool to browse and annotate metadata from RNA-Seq studies. / Kumar, Pankaj; Halama, Anna; Hayat, Shahina; Billing, Anja; Gupta, Manish; Yousri, Noha; Smith, Gregory M.; Suhre, Karsten.

In: BioMed Research International, Vol. 2015, 318064, 2015.

Research output: Contribution to journalArticle

@article{5b975bab01384beab18ea10fba636401,
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.",
author = "Pankaj Kumar and Anna Halama and Shahina Hayat and Anja Billing and Manish Gupta and Noha Yousri and Smith, {Gregory M.} and Karsten Suhre",
year = "2015",
doi = "10.1155/2015/318064",
language = "English",
volume = "2015",
journal = "BioMed Research International",
issn = "2314-6133",
publisher = "Hindawi Publishing Corporation",

}

TY - JOUR

T1 - MetaRNA-Seq

T2 - An interactive tool to browse and annotate metadata from RNA-Seq studies

AU - Kumar, Pankaj

AU - Halama, Anna

AU - Hayat, Shahina

AU - Billing, Anja

AU - Gupta, Manish

AU - Yousri, Noha

AU - Smith, Gregory M.

AU - Suhre, Karsten

PY - 2015

Y1 - 2015

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84941242278&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84941242278&partnerID=8YFLogxK

U2 - 10.1155/2015/318064

DO - 10.1155/2015/318064

M3 - Article

VL - 2015

JO - BioMed Research International

JF - BioMed Research International

SN - 2314-6133

M1 - 318064

ER -