ABSTRACT
In light of continuously accumulating data and knowledge on major human pathogens, comprehensive and up-to-date sources of easily accessible information are urgently required. The AureoWiki database (http://aureowiki.med.uni-greifswald.de) provides detailed information on the genes and proteins of clinically and experimentally relevant S. aureus strains, currently covering NCTC 8325, COL, Newman, USA300_FPR3757, and N315. By implementing a pan-genome approach, AureoWiki facilitates the transfer of knowledge gained in studies with different S. aureus strains, thus supporting functional annotation and better understanding of this organism. All data related to a given gene or gene product is compiled on a strain-specific gene page. The gene pages contain sequence-based information complemented by data on, for example, protein function and localization, transcriptional regulation, and gene expression. The information provided is connected via links to other databases and published literature. Importantly, orthologous genes of the individual strains, which are linked by a pan-genome gene identifier and a unified gene name, are presented side by side using strain-specific tabs. The respective pan-genome gene page contains an orthologue table for 32 S. aureus strains, a multiple-strain genome viewer, a protein sequence alignment as well as other comparative information. The data collected in AureoWiki is also accessible through various download options in order to support bioinformatics applications. In addition, based on two large-scale gene expression data sets, AureoWiki provides graphical representations of condition-dependent mRNA levels and protein profiles under various laboratory and infection-related conditions.
Subject(s)
Bacterial Proteins , Databases as Topic , Genes, Bacterial , Molecular Sequence Annotation , Staphylococcus aureus/genetics , Computational Biology , Genome, Bacterial , Internet , Staphylococcal Infections/microbiologyABSTRACT
From raw data to gene expression profiles, from single cultures to complex microbial communities, environmental proteomics works with data of different complexity levels that need to be interpreted in detail or in its entirety. Although data visualization is closely connected with data analysis approaches, this work will solely focus on data visualization. Complementing traditional tools such as bar charts or line graphs, scientists and visualization professionals have been provided sophisticated visualization tools. Many rules and concerns regarding the display of single but also complex data will be reviewed and discussed. Visual approaches such as microcharts, heat maps, stream graphs, and tree maps will be brought to the reader's attention and demonstrated by utilizing real data sets.
Subject(s)
Environmental Microbiology , Proteomics/methods , Statistics as Topic/methods , Bacterial Proteins/metabolism , Databases, Protein , Mass SpectrometryABSTRACT
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.
