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