GENCOM

An Excel Add-in for Genetic Composition Analysis Using Microarray Data

GENCOM is a new approach to the analysis of microarray hybridisation data derived from comparative genomic studies. This approach compares the fluorescence intensities from the hybridisation of differentially labelled DNA samples to DNA microarrays. Using statistical tests gene probes on the microarray are classified as either present or variable (i.e. divergent, partially deleted or absent). The analysis is based on a convergence algorithm that estimates the equality (regression) line fitted to the conserved genes, with the error inherent to the measurement technique. That error gives the basis to establish a boundary between present and variable genes, which is dynamically determined for each microarray. Moreover, variable genes are identified according to a statistical test taking into account both the average and variability of the replicates.

GENCOM is a user-friendly Excel add-in written in Visual Basic (Microsoft Excel 97 or above is required). GENCOM is part of the system used in-house at the Institute of Food Research to analyse microarray hybridisation data.

References

1. Pearson B.M., Pin C., Wright J., I'Anson K., Humphrey T., Wells J.M. (2003) Comparative genome analysis of Campylobacter jejuni using whole genome DNA microarrays. FEBS Lett 554: 224-230.

2. Pin C., Reuter M., Pearson B., Friis L., Overweg K., Baranyi J. and Wells, J. (2006): Comparison of different approaches for comparative genetic analysis using microarray hybidizations. Applied Microbiology and Biotechnology 72: 852-859

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