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

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  2. Dr Alison Graham
Author(s)Maleki-Dizaji S, Holcombe M, Rolfe MD, Fisher P, Green J, Poole RK, Graham AI
Publication type Article
JournalOnline Journal of Bioinformatics
Year2009
Volume10
Issue1
Pages51-59
ISSN (electronic)1443-2250
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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.
PublisherPestsearch International Pty. Ltd.
URLhttp://www.cpb.ouhsc.edu/ojvr/ecoliprintabs2009.htm
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