title: Protecs, a comprehensive and powerful storage and analysis system for OMICS data, applied for profiling the anaerobiosis response of Staphylococcus aureus COL.
abstract: Broad functional genomic studies call for comprehensive and powerful data repositories for storage of genome sequences, experimental information, protein identification data, protein properties and expression values. The better such data repositories can integrate and display complex data in a clear and structured way the more biologically meaningful conclusions or novel hypotheses can be derived from extensive omics data sets. This work presents the web accessible database system Protecs and how it was used to support analysis of 50 samples drawn from four Staphylococcus aureus cultivations under anaerobiosis. Protecs incorporates findings from visualization science, e.g. micro charts and heat maps in the user interface. Its integrated tools for expression data analysis in combination with TIGR Multi Experiment Viewer were used to highlight similar gene expression profiles in single or multiple experiments based on the continuously updated S. aureus master gel. Raw data analysis results are available online at www.protecs.uni-greifswald.de. Our meta-study revealed that S. aureus responds in different anaerobiotic experimental setups (growth without oxygen; growth without oxygen but with supplemental pyruvate and uracil; growth without oxygen but with NO(3)(-); growth without oxygen but with NO(3)(-) and without functional nreABC genes) with a general anaerobiosis response. Among others, this response is characterized by an induction of fermentation enzymes (PflB, Ldh1, SACOL0135, SACOL0660) as well as the response regulator SrrA. Interestingly, especially genes with a high codon adaptation index highly overlap with anaerobically induced genes.
authors.affiliation: Institute for Microbiology, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany.
authors.forename: Stephan
authors.initials: S
authors.lastname: Fuchs
authors.forename: Henry
authors.initials: H
authors.lastname: Mehlan
authors.forename: Harald
authors.initials: H
authors.lastname: Kusch
authors.forename: Alexander
authors.initials: A
authors.lastname: Teumer
authors.forename: Daniela
authors.initials: D
authors.lastname: Zühlke
authors.forename: Matthias
authors.initials: M
authors.lastname: Berth
authors.forename: Carmen
authors.initials: C
authors.lastname: Wolf
authors.forename: Thomas
authors.initials: T
authors.lastname: Dandekar
authors.forename: Michael
authors.initials: M
authors.lastname: Hecker
authors.forename: Susanne
authors.initials: S
authors.lastname: Engelmann
authors.forename: Jörg
authors.initials: J
authors.lastname: Bernhardt
mesh_terms: D000693:Anaerobiosis / Q000235:genetics / Q000502:physiology; D000704:Analysis of Variance; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D003628:Database Management Systems; D030541:Databases, Genetic; D005798:Genes, Bacterial; D020407:Internet; D012984:Software; D013211:Staphylococcus aureus / Q000235:genetics / Q000378:metabolism; D014584:User-Computer Interface
chemical_list: D001426:Bacterial Proteins