ArticleBMC genomics2005
A generic approach for the design of whole-genome oligoarrays, validated for genomotyping, deletion mapping and gene expression analysis on Staphylococcus aureus.
Article in BMC genomics, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
48 citing papers in PubMed, 104 citations in OpenAlex.
- Article
- The Disulfide Stress Response and ProteinAntioxidants (Basel, Switzerland) · 2019Article
- Genetic Adaptation of a Mevalonate Pathway Deficient Mutant inFrontiers in microbiology · 2018Article
- Daptomycin Tolerance in the Staphylococcus aureus pitA6 Mutant Is Due to Upregulation of the dlt Operon.Antimicrobial agents and chemotherapy · 2016Article
- Thiol-based redox switches in prokaryotes.Biological chemistry · 2015Review
- Staphylococcus epidermidis SrrAB regulates bacterial growth and biofilm formation differently under oxic and microaerobic conditions.Journal of bacteriology · 2015Article
- Emergence of a novel subpopulation of CC398 Staphylococcus aureus infecting animals is a serious hazard for humans.Frontiers in microbiology · 2014Article
- Importance of bacillithiol in the oxidative stress response of Staphylococcus aureus.Infection and immunity · 2014Article
- Microarray analysis of microbiota of gingival lesions in noma patients.PLoS neglected tropical diseases · 2013Article
- Article
- Geobacillus thermodenitrificans YjbH recognizes the C-terminal end of Bacillus subtilis Spx to accelerate Spx proteolysis by ClpXP.Microbiology (Reading, England) · 2012Article
- Global analysis of the Staphylococcus aureus response to mupirocin.Antimicrobial agents and chemotherapy · 2012Article
- The stringent response of Staphylococcus aureus and its impact on survival after phagocytosis through the induction of intracellular PSMs expression.PLoS pathogens · 2012Article
- Genome-wide transcriptional response of the archaeon Thermococcus gammatolerans to cadmium.PloS one · 2012Article
- Article
- S-bacillithiolation protects against hypochlorite stress in Bacillus subtilis as revealed by transcriptomics and redox proteomics.Molecular & cellular proteomics : MCP · 2011Article
- The σB-dependent yabJ-spoVG operon is involved in the regulation of extracellular nuclease, lipase, and protease expression in Staphylococcus aureus.Journal of bacteriology · 2011Article
- Daptomycin resistance mechanisms in clinically derived Staphylococcus aureus strains assessed by a combined transcriptomics and proteomics approach.The Journal of antimicrobial chemotherapy · 2011Article
- Open-target sparse sensing of biological agents using DNA microarray.BMC bioinformatics · 2011Article
- Role of the SaeRS two-component regulatory system in Staphylococcus epidermidis autolysis and biofilm formation.BMC microbiology · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundDNA microarray technology is widely used to determine the expression levels of thousands of genes in a single experiment, for a broad range of organisms. Optimal design of immobilized nucleic acids has a direct impact on the reliability of microarray results. However, despite small genome size and complexity, prokaryotic organisms are not frequently studied to validate selected bioinformatics approaches. Relying on parameters shown to affect the hybridization of nucleic acids, we designed freely available software and validated experimentally its performance on the bacterial pathogen Staphylococcus aureus.
resultsWe describe an efficient procedure for selecting 40-60 mer oligonucleotide probes combining optimal thermodynamic properties with high target specificity, suitable for genomic studies of microbial species. The algorithm for filtering probes from extensive oligonucleotides libraries fitting standard thermodynamic criteria includes positional information of predicted target-probe binding regions. This algorithm efficiently selected probes recognizing homologous gene targets across three different sequenced genomes of Staphylococcus aureus. BLAST analysis of the final selection of 5,427 probes yielded >97%, 93%, and 81% of Staphylococcus aureus genome coverage in strains N315, Mu50, and COL, respectively. A manufactured oligoarray including a subset of control Escherichia coli probes was validated for applications in the fields of comparative genomics and molecular epidemiology, mapping of deletion mutations and transcription profiling.
conclusionThis generic chip-design process merging sequence information from several related genomes improves genome coverage even in conserved regions.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.