This article is part of the supplement: Eleventh International Conference on Bioinformatics (InCoB2012): Computational Biology
Proceedings
An approach to identifying drug resistance associated mutations in bacterial strains
1 Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Poland
2 School of Computing, National University of Singapore, Singapore
BMC Genomics 2012, 13(Suppl 7):S23 doi:10.1186/1471-2164-13-S7-S23
Published: 13 December 2012Additional files
Additional file 1:
Collected phenotype and genotype data. Collected dataset of phenotypes (results of drug susceptibility tests). Columns represent drugs, rows represent S. aureus strains included in the study, put in the order corresponding to the reconstructed phylogenetical tree of strains. Green, yellow and red color cells represent collected information: susceptibility, intermediate resistance and resistance of isolates, respectively.
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Additional file 4:
Excel table with detailed results for point mutation profiles. Excel table providing results of our approach applied to point mutation profiles for ten drugs: penicillin, methicillin, oxacillin, tetracycline, clindamycin, erythromycin, gentamicin, ciprofloxacin, rifampicin and vancomycin
Format: XLSX Size: 1.9MB Download file
Additional file 2:
Summary table for the top scored gene gain/loss profiles (same thresholds as for Table 2 are applied). The columns refer to: gene identifier of the corresponding gene family; normalized weighted support (NWS); p-value and the drug resistance profiles put together with gene gain/loss profiles. Each cell in the gene gain/loss profiles corresponds to one strain, ordered according to the order in Figure 2. Cells corresponding to drug-resistant and drug-susceptible strains are colored red and green, respectively. Strains without drug resistance information are left white. For each gene gain/loss profile p and its corresponding row, if a cell in this row corresponds to strain i, such that rv(p) = p(i), then it is colored blue, otherwise it is colored pink.
Format: PDF Size: 59KB Download file
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Additional file 3:
Excel table with detailed results for gene gain/loss profiles. Excel table providing results of our approach applied to gene gain/loss profiles for ten drugs: penicillin, methicillin, oxacillin, tetracycline, clindamycin, erythromycin, gentamicin, ciprofloxacin, rifampicin and vancomycin.
Format: XLSX Size: 1.9MB Download file
Additional file 5:
Table with point mutation profiles for top scored mutations profiles. Summary table for the top scored gene point mutation profiles (same thresholds as for Table 3 are applied). The columns refer to: gene identifier of the corresponding gene family; normalized weighted support (NWS); p-value and the drug resistance profiles put together with point mutation profiles. Each cell in the point profiles corresponds to one strain, ordered according to the order in Figure 2. Cells corresponding to drug-resistant and drug-susceptible strains are colored red and green, respectively. Strains without drug resistance information are left white. For each point mutation profile p and its corresponding row, if a cell in this row corresponds to strain i (assuming the corresponding gene is present in the strain sequence), such that rv(p) = p(i), then it is colored blue, otherwise it is colored pink. Cells corresponding to strains without the corresponding gene are left white.
Format: PDF Size: 76KB Download file
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