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Online Journal of Bioinformatics ©
Volume 10(1):51-59, 2009.
A systematic approach to understanding Escherichia coli responses to oxygen:
From microarray raw data to pathways and published abstracts
Maleki-Dizaji S1,*, Holcombe M1, Rolfe MD2, Fisher P3, Green J2, Poole RK2, Graham AI2, SYSMO-SUMO consortium4
Computer Science, The
Maleki-Dizaji S, Holcombe M, Rolfe MD, Fisher P, Green J, Poole RK, Graham AI, A Systematic Approach to Understanding Escherichia coli Responses to Oxygen: From Microarray Raw Data to Pathways and Published Abstracts, Online J Bioinformatics, 10(1):51-59, 2009. 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.
Keywords: E. coli, Microarray, Taverna Workflow, Web Services.