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From proteomics to systems biology of bacterial pathogens: Approaches, tools, and applications
Author(s) -
Plikat Uwe,
Voshol Hans,
Dangendorf Yvonne,
Wiedmann Brigitte,
Devay Piroska,
Müller Dieter,
Wirth Urs,
Szustakowski Joseph,
Chirn GungWei,
Inverardi Bruno,
Puyang Xiaoling,
Brown Kara,
Kamp Heather,
Hoving Sjouke,
Ruchti Alexandra,
Brendlen Nathalie,
Peterson Ron,
Buco Jennifer,
Oostrum Jan van,
Peitsch Manuel C.
Publication year - 2007
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.200600925
Subject(s) - ensembl , systems biology , computational biology , proteome , visualization , computer science , biology , proteomics , software , data integration , genome , genomics , bioinformatics , data science , gene , data mining , genetics , programming language
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.