. 2012 Jan 24;40(10):4320–4333. doi: 10.1093/nar/gks017

Table 1.

Whole-genome location analysis of oxidative stress sensor OxyR in Pseudomonas aeruginosa (cutoff >1.0)

PA no.^a	Gene^a	ChIP-chip			Binding motif			Gene product^a
PA no.^a	Gene^a	Max. Enrich.	Distance to ATG	Genes affected^a	Conserved motif^b	Distance to ATG^b	PMW score^b	Gene product^a
PA0139	ahpC	1.72	171	1	ATAGATTTAGATAAT	101	7.71	Alkyl hydroperoxide reductase subunit C
PA0140	ahpF	1.72	127	1				Alkyl hydroperoxide reductase subunit F
PA4236	katA	1.61	260	2	ATTGATCTCGCTTAT	116	7.35	Catalase
PA5345	recG	1.59	738	1				ATP-dependent DNA helicase RecG
PA0962	dps	1.02	107	1	ATAGGGAGAATCTAT	107	7.66	Probable DNA-binding stress protein
PA2146		1.04	287	1	ATCTTTGAACCCTAT	153	7.02	Conserved hypothetical protein
PA2050		1.27	202	2	AAAAAGAATATTAAT	171	6.26	Probable ECF sigma-factor
PA2054	cynR	1.07	13	1	ATTGGTCTGGTCTAT	15	7.36	Transcriptional regulator
PA3135		1.22	-1	2	AAGTGTAGCGCCTAT	31	6.09	Probable transcriptional regulator
PA0717		1.23	306	3	ATAGAGCAAGACTAT	352	7.59	Hypothetical protein of bacteriophage Pf1
PA4406.1		1.27		1				sRNA
PA0195	pntAA	1.17	289	1	ATTAAAAACATTAAT	354	6.81	Putative NAD(P) transhydrogenase. subunit alpha part 1
PA0903	alaS	1.42	106	1	ATAGTTATTGCCTAT	92	7.77	Alanyl-tRNA synthetase
PA0963	aspS	1.02	304	2	ATAGGGAGAATCTAT	319	7.66	Aspartyl-tRNA synthetase
PA1054		1.48	271	6	ATAGATTGCGATAAT	138	7.45	Probable NADH dehydrogenase
PA1541		1.20	308	2	ATCGATTGGCTTTTT	237	6.36	Probable drug efflux transporter
PA2053	cynT	1.07	102	2	ATTGGTCTGGTCTAT	86	7.36	Carbonate dehydratase
PA3032	snr1	1.34	282	2	ATAGACTCAGGCTAT	201	7.53	Cytochrome c Snr1
PA3136		1.22	71	2	AAGTGTAGCGCCTAT	25	6.09	Probable secretion protein
PA4268	rpsL	1.23	76	1	ATAGCTCCACTGATT	3	6.17	30S ribosomal protein S12
PA4406	lpxC	1.27	123	1	ACTGTTTTCAACAAT	30	6.50	UDP-3-O-acyl-N-acetylglucosamine deacetylase
PA5291		1.36	103	1	ATCGTGATAGCTAAT	64	7.12	Probable choline transporter
PA0938		1.27	16	1	ATCATCGGTAGTTAT	96	6.67	Hypothetical protein
PA2044		1.25	101	1	ATTGATAAAACCTAT	95	7.84	Hypothetical protein
PA2145		1.04	8	1	ATAGACCCATTCAAT	38	7.23	Hypothetical protein
PA2595		1.13	8	1				Conserved hypothetical protein

^aChIP-enriched OxyR-binding regions are shown by the PA number of the associated genes; the respective gene names, operon compositions (indicated by the number of affected genes) and gene annotations are extracted from http://www.pseudomonas.com.

^bConserved motifs, distance to ATG and the PMW scores were all obtained by Virtual Footprint (as described in ‘Materials and Methods’ section) for the entire genome of P. aeruginosa PAO1 using regions with cutoff >0.5 as the PMW entry; the defined motifs in Supplementary Table S1 were chosen based on those motifs with the highest PMW scores for each binding region.