COnTORT: COmprehensive Transcriptomic ORganizational Tool for Simultaneously Retrieving and Organizing Numerous Gene Expression Data Sets from the NCBI Gene Expression Omnibus Database-Reference-Cited by-同舟云学术

COnTORT: COmprehensive Transcriptomic ORganizational Tool for Simultaneously Retrieving and Organizing Numerous Gene Expression Data Sets from the NCBI Gene Expression Omnibus Database

Published:2020-06-18 Issue:25 Volume:9 Page:
ISSN:2576-098X
Container-title:Microbiology Resource Announcements
language:en
Short-container-title:Microbiol Resour Announc

Author:

Myers Kevin S.¹^ORCID,Place Michael¹,Noguera Daniel R.¹²^ORCID,Donohue Timothy J.¹³^ORCID

Affiliation:

1. Wisconsin Energy Institute and Great Lakes Bioenergy Research Center, University of Wisconsin—Madison, Madison, Wisconsin, USA

2. Department of Civil & Environmental Engineering, University of Wisconsin—Madison, Madison, Wisconsin, USA

3. Department of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USA

Abstract

We introduce COnTORT ( CO mprehensive T ranscriptomic OR ganizational T ool), a publicly available program that retrieves all available gene expression data and associated metadata for an organism from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database. The data are compiled into text files that can be used for downstream bioinformatic applications.

Funder

U.S. Department of Energy

Publisher

American Society for Microbiology

Subject

Genetics,Immunology and Microbiology (miscellaneous),Molecular Biology

Link

https://journals.asm.org/doi/pdf/10.1128/MRA.00587-20

Reference6 articles.

1. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

2. NCBI GEO: archive for functional genomics data sets—update

3. NCBI GEO: mining tens of millions of expression profiles--database and tools update

4. GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor

5. GenBank

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