TABLE 4.

Gene set enrichment analysis of hypothesized protective mechanisms and other stress responses in drip-flow reactor P. aeruginosa biofilms

Mechanisma	P value for overlap with genes		Reference(s)
	Up in biofilm	Down in biofilm
Efflux pumps	0.916	0.994	53
Peroxide stress	0.071	1.000	48–51
SOS response	1.000	0.861	52
Heat shock and chaperones	0.852	0.012	53
Fe limitation	0.896	0.997	55, 55
Cyclic-di-GMP	0.910	0.957	56
Toxin-antitoxin modules	1.000	1.000	57
Planktonic sensitivity to CIP	0.364	0.256	58
Planktonic tolerance to CIP	0.965	0.020	59
Planktonic sensitivity to TOB	1.000	0.017	59
Response to TOB in DFB, up	0.993	1.63 × 10−8	Table S2
Response to TOB in DFB, down	<1 × 10−14	0.994	Table S2
Response to CIP in DFB, up	0.993	0.051	Table S2
Response to CIP in DFB, down	1.50 × 10−9	0.861	Table S2
Oxygen limitation	<1 × 10−14	1.000	62
Oxygen downshift	<1 × 10−14	1.000	63
Stationary phase	<1 × 10−14	1.000	62, 96–98
HSL quorum sensing	0.004	1.000	69–71
Osmotic stress	1.11 × 10−4	1.000	72

^aCIP, ciprofloxacin; TOB, tobramycin; DFB, drip-flow biofilm; HSL, homoserine lactone.