Open Access Research article

Colon cancer associated genes exhibit signatures of positive selection at functionally significant positions

Claire C Morgan12, Kabita Shakya123, Andrew Webb12, Thomas A Walsh12, Mark Lynch124, Christine E Loscher4, Heather J Ruskin23 and Mary J O’Connell12*

Author Affiliations

1 Bioinformatics and Molecular Evolution Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland

2 Centre for Scientific Computing & Complex Systems Modelling (SCI-SYM), Dublin City University, Glasnevin, Dublin 9, Ireland

3 School of Computing, Dublin City University, Glasnevin, Dublin 9, Ireland

4 Immunomodulatory Research Group, School of Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland

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BMC Evolutionary Biology 2012, 12:114  doi:10.1186/1471-2148-12-114

Published: 12 July 2012

Additional files

Additional file 1:

Details of the data used in the analysis, the 21 species and their genome coverage. Orthologs that were not found by the Ensembl genome browser are labeled in black, orthologs identified are shown in white.

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Additional file 2:

Complete set of all multiple sequence alignments used in the analysis. The data is presented on a gene-by-gene basis in nexus format.

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Additional file 3:

Likelihood ratio tests performed and their associated significance values.

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Additional file 4:

Full set of models, associated likelihood scores and parameter estimates for all genes in the colon cancer gene dataset. This information is given alphabetically on a gene-by-gene basis. All estimated parameters, Likelihood values and BEB or NEB sites are listed.

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Additional file 5:

Full set of recombination test results on a per gene and per species basis. The value highlighted in yellow for TP53 represents a region where recombination was detected with reasonable confidence that also coincided with a positively selected residue (i.e. false positive).

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