. 2016 Apr 6;1(2):e00042-16. doi: 10.1128/mSphere.00042-16

TABLE 2 .

Description of discussed genes and biological processes

Biological process or category and gene	Symbol	Description	Biofilm, 48 h			Biofilm, 120 h
Biological process or category and gene	Symbol	Description	Regulation status	logFC	FDR	Regulation status	logFC	FDR
DNA replication
LEPBI_I0001	dnaA	Chromosomal replication initiator protein	Down	−0.3	5e−3
LEPBI_I0012		DNA polymerase III, delta subunit	Down	−0.35	3e−3
LEPBI_I3461	dnaX1	DNA polymerase III, gamma subunit	Down	−0.4	9e−5
LEPBI_I3479	dnaX2	DNA polymerase III, tau subunit	Down	−0.45	7e−4
LEPBI_I3473	parB	Chromosome partitioning protein ParB	Down	−0.3	4e−3
LEPBI_II0026	parB	Chromosome partitioning protein ParB	Down	−0.39	1e−3
LEPBI_I3477	gidA	Glucose-inhibited partition protein A	Down	−0.38	5e−4
LEPBI_I3475	gidB	Glucose-inhibited partition protein B	Down	−0.31	5e−3
LEPBI_I0003	recF	DNA replication and repair protein RecF	Down	−0.4	1e−4
LEPBI_I0005	gyrB1	DNA gyrase subunit B	Down	−0.3	2e−3
Cell growth
LEPBI_I2249	vagC	Putative virulence- associated protein B	Up	0.9	2e−5
LEPBI_I3440	hepA	ATP-dependent RNA helicase	Down	−0.4	1e−5
LEPBI_I0011	fis	Fis family transcriptional regulator	Down	−0.45	4e−3	Down	−0.5	3e−4
LEPBI_I3348		Pyrroloquinoline quinone	Down	−0.35	3e−4
Motility
LEPBI_I0008		PilZ domain	Down	−0.31	9e−3
LEPBI_II0088		PilZ domain	Down	−0.5	9e−5	Down	−0.44	1e−3
LEPBI_I0917	cheY1	Chemotactic response regulator CheY	Up	0.47	6e−5
LEPBI_I1764	cheR	Chemotaxis protein methyltransferase	Down	−0.37	1e−3
LEPBI_I1589	flaB1	Flagellar filament core protein FlaB	Up	1.19	8e−19
LEPBI_I2133	flaB2	Flagellar filament 35-kDa core protein	Up	0.66	4e−9
LEPBI_I2132	flaB3	Flagellar filament 35-kDa core protein	Up	0.98	4e−12
LEPBI_I2335	flaA1	Flagellar filament outer layer protein A	Up	0.33	6e−3
Outer membrane proteins
LEPBI_Ia0817	ompL1	Outer membrane protein OmpL1	Up	0.88	2e−21	Up	0.31	3e−3
LEPBI_I1873		OmpA-like protein	Up	0.38	3e−3
LEPBI_I0009		Putative lipoprotein	Up	0.35	2e−3
LEPBI_I1822		Putative LipL31	Up	0.38	5e−3
LEPBI_2674	lntB	Apolipoprotein N-acyltransferase LntB	Up	0.64	8e−9
Sugar metabolism
LEPBI_I0073	galK	Galactokinase	Down	−0.48	9e−7
LEPBI_I0113	galE	Putative UDP-glucose 4-epimerase	Down	−0.32	9e−4
LEPBI_I0037		Putative transferase	Up	0.37	1e−3
LEPBI_I2021		Putative capsule polysaccharide biosynthesis protein	Up	0.32	8e−3
LEPBI_II0277	algI	O-Acetyltransferase AlgI	Down	−0.38	5e−4
LEPBI_I3464		Putative alginate export protein	Down	−0.36	1e−3
Lipid metabolism
LEPBI_I0107		Long-chain fatty acid–CoA ligase	Down	−0.46	9e−6
LEPBI_I0104	acdA1	Acyl-CoA dehydrogenase	Down	−0.33	1e−3
LEPBI_I0052		Enoyl-CoA hydratase	Down	−0.36	4e−4
LEPBI_I0777		Putative triglyceride lipase	Up	0.69	1.5e−6
LEPBI_II0198	fabG	3-Oxoacyl-ACP reductase	Down	−0.45	7e−7
LEPBI_II0199	fabG	3-Oxoacyl-ACP reductase	Down	−0.39	4e−3
LEPBI_II0211	fabG	3-Oxoacyl-ACP reductase	Down	−0.38	2e−3
Iron metabolism
LEPBI_I1883	fecA	Iron(III) dicitrate TonB-dependent receptor	Up	0.5	2e−5
LEPBI_I2760	NA^a	Putative TonB- dependent receptor protein	Up	0.38	1.5e−5
LEPBI_I3362	NA	TonB-dependent receptor protein	Down	−0.32	2.7e−3
LEPBI_I0669	hemO	Heme oxygenase HemO	Up	0.5	1.4e−5
LEPBI_p0012	hemS	Hemin degradation protein HemS	Up	0.69	5e−4
LEPBI_p0015	hemT	ABC-type Fe³⁺-hydroxamate transport system				Up	0.48	3e−4
LEPBI_p0014	hemU	ABC-type hemin transport system, permease				Up	0.63	8e−7
LEPBI_p0013	hemV	ABC-type hemin transport system, ATPase				Up	1.1	6e−21
LEPBI_I2375	NA	Hemolysin	Up	0.4	1e−3
Regulators
LEPBI_I1327	flgM	Anti-sigma factor FlgM	Up	0.7	1e−7
LEPBI_I2676	carD	CarD family transcriptional regulator	Up	0.86	3e−12	Up	0.65	1.9e−7
LEPBI_I1529	pnp	Polynucleotide phosphorylase/polyadenylase	Up	0.38	7e−3
LEPBI_I1944	adk	Adenylate kinase	Up	1.2	4e−9	Up	0.72	5e−4
LEPBI_I1460	fecR	FecR protein	Up	0.76	6e−11	Up	0.44	2e−4
Uncharacterized genes
LEPBI_I0858	NA	Putative lipase	Up	1.5	8.5e−9
LEPBI_I0859	NA	Putative lipase	Up	1.35	8.5e−30

NA, not available.