Open Access Highly Accessed Research article

The evolutionary rate of antibacterial drug targets

Arkadiusz Gladki1, Szymon Kaczanowski1, Pawel Szczesny12 and Piotr Zielenkiewicz12*

Author Affiliations

1 Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, Warsaw, Poland

2 Department of Plant Molecular Biology, Institute of Experimental Plant Biology and Biotechnology, University of Warsaw, Warsaw, Miecznikowa 1

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BMC Bioinformatics 2013, 14:36  doi:10.1186/1471-2105-14-36

Published: 1 February 2013

Additional files

Additional file 1:

Essentiality and ranking of known drug targets. The essentiality and ranking (from an evolutionary perspective) of known drug targets. Drug targets are ordered by drug class. Data for eight species of interest are presented in separate columns. Red: essential genes, blue: nonessential genes, grey: no data addressing essentiality, white: no ortholog with reliable omega.

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Additional file 2:

Statistical data - pN/pS analysis. Mean pN/pS ratio for three sets of genes (ADT - drug targets, ESS - essential genes, ALL - other genes) presented. Data for eight species analyzed in the study. P-values where corrected for multiple testing with FDR (Benjamini-Yekutieli algorithm). Abbreviations: ciu - confidence interval upper limit; cil - confidence interval lower limit, eco – Escherichia coli, ftn – Francisella novicida, hin – Haemophilus influenzae, hpy – Helicobacter pylori, pau – Pseudomonas aeruginosa, sao – Staphylococcus aureus, spn – Streptococcus pneumoniae, stm – Salmonella typhimurium.

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Additional file 3:

Statistical data - dN/dS analysis. Mean dN/dS ratio for three sets of genes (ADT - drug targets, ESS - essential genes, ALL - other genes) presented. Data for eight species analyzed in the study. P-values where corrected for multiple testing with FDR (Benjamini-Yekutieli algorithm). Abbreviations: ciu - confidence interval upper limit; cil - confidence interval lower limit, eco – Escherichia coli, ftn – Francisella novicida, hin – Haemophilus influenzae, hpy – Helicobacter pylori, pau – Pseudomonas aeruginosa, sao – Staphylococcus aureus, spn – Streptococcus pneumoniae, stm – Salmonella typhimurium.

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Additional file 4:

Dn/Ds analysis - materials, methods and results. Analysis of evolutionary rate (dN/dS ratio) of known drug targets. Materials and methods as well as Results are presented in the file. Details about recombination (detection and removal procedures) can be also found.

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