TABLE 3.

Significantly down-regulated genes at pH 9 in S. aureus COL biofilm-associated (A) and planktonic cells (B) (p < 0.05).

Function	Gene name	Gene number (in S. aureus COL)	Gene annotation	log2 fold-change	p-Value
(A)
Transcription regulators	airR	SACOL1905	ref | NP_388770.1 Predicted transcriptional regulator	−3.34	0.0042
	degU	SACOL2389	ref| NP_714049.1 Two-component response regulator transcriptional regulator protein	−3.32	0.0015
	phoU-like	not found	ref | NP_337929.l| Phosphate transport system regulator PhoU-related protein	−3.28	0.0023
Biofilm formation	mapW	SACOL0985	emb | CAB51S07.1 Cell surface protein Map-W	−3.24	0.0014
(B)
Transcription regulators	sarA	SACOL0672	gb | AAM74164.11 AF515775_2 Staphylococcal accessory regulator variant	−3.43	0.0317
	agrB	SACOL2023	ref | NP_469388.1 Similar to Staphylococcus two-component sensor histidine kinase AgrB	−3.38	0.0187
Biofilm-related proteins	mntC	SACOL0638	NP_720653 a surface adhesion precursor	−3.34	0.0042
Cell wall-related enzymes	murAB	SACOL2116	sp | Q99SD4| MUA2_STAAM UDP-N-acetylglucosamine 1-carboxyvinyltransferase 2 (Enoylpyruvate transferase 2)	−3.33	0.0068
	lytM	SACOL0263	pir| F89791 Peptidoglycan hydrolase	−3.33	0.0109
Antigen - Toxin - Virulence	sek	SACOL0336	gb | AAC2S96S.1 Staphylococcal enterotoxin K	−3.45	0.0036
Drug resistance	mdeA/emrB	SACOL2413	ref| NP_375526.l| MFS transporter; drug resistance transporter EmrB/QacA subfamily	−3.34	0.0042
General functions [transporters, DNA-RNA, general]	yozE- like	SACOL2556	ref | NP_375656-11 hypothetical protein, similarto secretory antigen precursorSsaA	−4.19	0.0461
	parC	SACOL1390	ref | NP_758033.1 DNA topoisomerase IV subunit A	−3.33	0.0065
	–	not found	ref | NP_720897.1 Putative cell division protein	−3.33	0.0068
	maoC	not found	ref | NP_280923.1 Monoamine oxidase regulatory-like	−3.31	0.0095

The genes have been ranked according to their log₂ fold change (pH5/pH7) value in each functional category.