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A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes
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. Alth...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2008
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2262894/ https://www.ncbi.nlm.nih.gov/pubmed/18230148 http://dx.doi.org/10.1186/1471-2164-9-53 |
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author | Carter, Ben Wu, Guanghui Woodward, Martin J Anjum, Muna F |
author_facet | Carter, Ben Wu, Guanghui Woodward, Martin J Anjum, Muna F |
author_sort | Carter, Ben |
collection | PubMed |
description | 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. CONCLUSION: 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. |
format | Text |
id | pubmed-2262894 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-22628942008-03-05 A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes Carter, Ben Wu, Guanghui Woodward, Martin J Anjum, Muna F BMC Genomics Methodology Article 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. CONCLUSION: 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. BioMed Central 2008-01-29 /pmc/articles/PMC2262894/ /pubmed/18230148 http://dx.doi.org/10.1186/1471-2164-9-53 Text en Copyright © 2008 Carter et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methodology Article Carter, Ben Wu, Guanghui Woodward, Martin J Anjum, Muna F A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes |
title | A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes |
title_full | A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes |
title_fullStr | A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes |
title_full_unstemmed | A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes |
title_short | A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes |
title_sort | process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2262894/ https://www.ncbi.nlm.nih.gov/pubmed/18230148 http://dx.doi.org/10.1186/1471-2164-9-53 |
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