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A systematic approach to understanding Escherichia coli responses to oxygen: from microarray raw data to pathways and published abstracts

Lookup NU author(s): Dr Alison GrahamORCiD


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Genome-wide transcript-profiling has transformed the study of gene regulation in bacteria and other organisms. However, analyses of these microarray datasets to identify regulons, pathways and relevant literature are often user-intensive. Here, a transcript-profiling study comparing Escherichia coli cultures from aerobic and anaerobic conditions is used to develop a data-driven methodology that identifies the known metabolic pathways and regulons present in a set of differentially expressed genes. These are subsequently used to obtain a corpus of published abstracts (from the PubMed database) relating to each biological pathway. Thus, the workflow facilitates consistent and user-friendly interrogation of transcriptomic datasets allowing experimentalists to focus on advanced data analysis and interpretational tasks.

Publication metadata

Author(s): Maleki-Dizaji S, Holcombe M, Rolfe MD, Fisher P, Green J, Poole RK, Graham AI

Publication type: Article

Publication status: Published

Journal: Online Journal of Bioinformatics

Year: 2009

Volume: 10

Issue: 1

Pages: 51-59

Print publication date: 03/03/2011

ISSN (electronic): 1443-2250

Publisher: Pestsearch International Pty. Ltd.