title: A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes.
abstract: BACKGROUND
  Microarray based comparative genomic hybridisation (CGH) experiments have been used to study numerous biological problems including understanding genome plasticity in pathogenic bacteria. Typically such experiments produce large data sets that are difficult for biologists to handle. Although there are some programmes available for interpretation of bacterial transcriptomics data and CGH microarray data for looking at genetic stability in oncogenes, there are none specifically to understand the mosaic nature of bacterial genomes. Consequently a bottle neck still persists in accurate processing and mathematical analysis of these data. To address this shortfall we have produced a simple and robust CGH microarray data analysis process that may be automated in the future to understand bacterial genomic diversity.
  
  
  RESULTS
  The process involves five steps: cleaning, normalisation, estimating gene presence and absence or divergence, validation, and analysis of data from test against three reference strains simultaneously. Each stage of the process is described and we have compared a number of methods available for characterising bacterial genomic diversity, for calculating the cut-off between gene presence and absence or divergence, and shown that a simple dynamic approach using a kernel density estimator performed better than both established, as well as a more sophisticated mixture modelling technique. We have also shown that current methods commonly used for CGH microarray analysis in tumour and cancer cell lines are not appropriate for analysing our data.
  
  
  CONCLUSIONS
  After carrying out the analysis and validation for three sequenced Escherichia coli strains, CGH microarray data from 19 E. coli O157 pathogenic test strains were used to demonstrate the benefits of applying this simple and robust process to CGH microarray studies using bacterial genomes.
authors.affiliation: Department of Food and Environmental Safety, Veterinary Laboratories Agency-Weybridge, New Haw, Addlestone, Surrey KT15 3NB, UK. b.carter@vla.defra.gsi.gov.uk
authors.forename: Ben
authors.initials: B
authors.lastname: Carter
authors.forename: Guanghui
authors.initials: G
authors.lastname: Wu
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Woodward
authors.forename: Muna F
authors.initials: MF
authors.lastname: Anjum
mesh_terms: D000465:Algorithms; D003627:Data Interpretation, Statistical; D004926:Escherichia coli / Q000145:classification / Q000235:genetics*; D048168:Escherichia coli K12 / Q000235:genetics; D019453:Escherichia coli O157 / Q000235:genetics; D018628:Gene Dosage; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods* / Q000706:statistics & numerical data; D015233:Models, Statistical; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000706:statistics & numerical data; D012680:Sensitivity and Specificity; D013045:Species Specificity