Identifying genetic determinants of complex phenotypes from whole genome sequence data

BMC Genomics

Table 3 Gene lists of the most important candidates for drug resistance in P.aeruginosa

Drug	Setting 1	Setting 2	Setting 3
Ciprofloxacin	trpI, transcriptional regulator TrpI	hypothetical protein	trpI, transcriptional regulator TrpI
	lysin domain-containing protein	HIS/PHE ammonia-lyase	tag, DNA-3-methylad. glycosidase I
	tag, DNA-3-methylad. glycosidase I	LysR family transcriptional regulator	lysin domain-containing protein
	recF, recombination protein F		glutamine synthetase
	D,D-heptose 1,7-bisphos. phosphatase		hypothetical protein
Ceftazidime	hemolysin activ./secret. prot	hypothetical protein (PA_40040)	hemolysin activ./secret. prot
	hypothetical protein (PA_40040)	sensor/response regulator hybrid	hypothetical protein (PA_40040)
	gyrB, DNA gyrase subunit B		gyrB, DNA gyrase subunit B
			hemagglutinin
			recQ, ATP-depend. DNA helicase
Gentamicin	Rossmann fold nucleotide-bind. prot.	sbrR, SbrR	tonB2, hypothetical protein
	gyrB, DNA gyrase subunit B	tonB2, hypothetical protein	hemagglutinin
	hemagglutinin	hemagglutinin	sbrR, SbrR
	acyltransferase	tufA, elongation factor Tu	hemolysin activ./secret. prot
	tonB2, hypothetical protein	hemolysin activ./secret. prot
	nirN, c-type cytochrome

Shown are the genes identified in all four runs under the four settings defined in Table 2. For each drug, the genes identified in all three settings are highlighted (boldface), as well as those found in two out of the three settings (italics). Gene names that are underlined (setting 1 only) are those identified during the cross-validation experiment, under both chunk sizes

ISSN: 1471-2164