©1996-2009 All Rights
Reserved. Online Journal of Bioinformatics.
OJBTM
Online Journal
of Bioinformatics ©
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, (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.