From proteomics to systems biology of bacterial pathogens: approaches, tools, and applications.
The hallmark of a systems biology approach is the integration of computational tools with experimental data encompassing multiple classes of biomolecules across different functional levels. Equally important as the availability of reasonably comprehensive information at the gene, protein, and metabolite levels is the development of adequate analysis and visualization tools to reduce the inherent complexity to interpretable dimensions. In this paper, we describe the integration of a 2-D gel-based proteome map of Staphylococcus aureus Mu50 with genomic and transcriptomic information through a customized data integration and user interface built on the Ensembl genome browser. We illustrate its application and potential through the analysis of a defined system perturbation caused by a mutation in the formyltransferase gene. We envision that this software package, which we called Insieme, can support the development of novel antibiotics by allowing a systems-based view of the bacterial response pathways.
Plikat
Uwe
U
Department of Genome and Proteome Sciences, Novartis Institutes for BioMedical Research, Basel, Switzerland. uwe.plikat@novartis.com
Voshol
Hans
H
Dangendorf
Yvonne
Y
Wiedmann
Brigitte
B
Devay
Piroska
P
Müller
Dieter
D
Wirth
Urs
U
Szustakowski
Joseph
J
Chirn
Gung-Wei
GW
Inverardi
Bruno
B
Puyang
Xiaoling
X
Brown
Kara
K
Kamp
Heather
H
Hoving
Sjouke
S
Ruchti
Alexandra
A
Brendlen
Nathalie
N
Peterson
Ron
R
Buco
Jennifer
J
Oostrum
Jan van
Jv
Peitsch
Manuel C
MC
D001419:Bacteria / Q000472:pathogenicity*; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D015180:Electrophoresis, Gel, Two-Dimensional; D020411:Oligonucleotide Array Sequence Analysis; D020543:Proteome / Q000032:analysis; D040901:Proteomics / Q000379:methods; D020539:Sequence Analysis, Protein; D012984:Software; D013211:Staphylococcus aureus; D049490:Systems Biology
D001426:Bacterial Proteins; D020543:Proteome