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OJBTM
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
1Department of
Computer Science, The
ABSTRACT
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.