title: From proteomics to systems biology of bacterial pathogens: approaches, tools, and applications.
abstract: 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.
authors: Department of Genome and Proteome Sciences, Novartis Institutes for BioMedical Research, Basel, Switzerland. uwe.plikat@novartis.com
authors: Uwe
authors: U
authors: Plikat
authors: Hans
authors: H
authors: Voshol
authors: Yvonne
authors: Y
authors: Dangendorf
authors: Brigitte
authors: B
authors: Wiedmann
authors: Piroska
authors: P
authors: Devay
authors: Dieter
authors: D
authors: Müller
authors: Urs
authors: U
authors: Wirth
authors: Joseph
authors: J
authors: Szustakowski
authors: Gung-Wei
authors: GW
authors: Chirn
authors: Bruno
authors: B
authors: Inverardi
authors: Xiaoling
authors: X
authors: Puyang
authors: Kara
authors: K
authors: Brown
authors: Heather
authors: H
authors: Kamp
authors: Sjouke
authors: S
authors: Hoving
authors: Alexandra
authors: A
authors: Ruchti
authors: Nathalie
authors: N
authors: Brendlen
authors: Ron
authors: R
authors: Peterson
authors: Jennifer
authors: J
authors: Buco
authors: Jan van
authors: Jv
authors: Oostrum
authors: Manuel C
authors: MC
authors: Peitsch
mesh_terms: 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
chemical_list: D001426:Bacterial Proteins; D020543:Proteome