. 2023 Jun 24;17(9):1430–1444. doi: 10.1038/s41396-023-01456-3

Table 2.

List of genes significant in the correlation analysis and at least one of the differential expression analyses.

Gene	COG	Product	Localization	Correlation with MV number	log₂FC SK36 Suc/Glu O₂	log₂FC SK36 Suc/Glu N₂	log₂FC Pg + SK36/SK36
SSA_0140	P	Copper-translocating P-type ATPase, putative ctpA	CytoplasmicMembrane	0.42	−0.75	NS	NS
SSA_0204	TK	Nisin biosynthesis two-component response transcriptional regulator nisR, putative	Cytoplasmic	0.4	−1.16	NS	NS
SSA_0205	T	NisK (sensor-receptor histidine kinase domain), putative	CytoplasmicMembrane	0.52	NS	NS	−1.25
SSA_0917	E	Cobalamin-independent methionine synthase II, putative	Cytoplasmic	0.39	−0.9	NS	−0.67
SSA_1035	S	Pyrimidine nucleoside phosphorylase, putative pdp	Cytoplasmic	0.49	−1.35	NS	NS
SSA_1036	F	Deoxyribose-phosphate aldolase, putative deoC	Cytoplasmic	0.4	−1.42	NS	NS
SSA_1038	F	Lipoprotein, putative	Unknown	0.51	−1.29	−0.77	NS
SSA_1039	R	Sugar ABC transporter, ATP-binding protein, putative	CytoplasmicMembrane	0.54	−1.15	NS	−0.77
SSA_1040	R	Sugar ABC transporter, permease protein, putative	CytoplasmicMembrane	0.49	NS	−0.78	−1.16
SSA_1369	V	FmtA-like protein, putative	CytoplasmicMembrane	0.51	NS	−1.37	NS
SSA_1371	V	FmtA-like protein, putative	CytoplasmicMembrane	0.54	NS	−1.04	NS
SSA_1571	J	Threonyl-tRNA synthetase, thrS	Cytoplasmic	0.43	−1.31	NS	NS
SSA_1572	S	Conserved hypothetical protein	Cytoplasmic	0.43	−1.81	−1.3	NS
SSA_1679	V	ABC-type multidrug transport system, ATPase component, putative cylA	CytoplasmicMembrane	0.54	−0.68	NS	NS
SSA_1918	G	Phosphotransferase system, mannose-specific EIIAB, putative	Cytoplasmic	0.44	−1.24	NS	NS
SSA_1919	G	Phosphotransferase system, mannose-specific EIIC, putative	CytoplasmicMembrane	0.43	−1.05	NS	NS
SSA_1920	G	Phosphotransferase system, mannose-specific EIID, putative	CytoplasmicMembrane	0.39	−1.17	NS	NS
SSA_1961	K	Transcriptional regulator, XRE family, putative	Cytoplasmic	0.45	NS	NS	−0.69
SSA_2153	R	ABC-type transporter (uncharacterized), permease component, putative	CytoplasmicMembrane	0.48	NS	NS	−1.4
SSA_2189	O	Conserved hypothetical protein	Cytoplasmic	0.44	NS	NS	−0.98
SSA_0265	X	ORFA, transposon ISSsa1	Cytoplasmic	−0.45	1.18	1.14	NS
SSA_0287	C	Glycerol dehydrogenase, NAD+ dependent, putative gldA	Cytoplasmic	−0.44	1.05	NS	NS
SSA_0329	G	Glycerol uptake facilitator/aquaporin protein, putative	CytoplasmicMembrane	−0.58	1.71	NS	NS
SSA_0330	S	Membrane protein, putative	CytoplasmicMembrane	−0.45	0.97	NS	NS
SSA_0332	R	Conserved hypothetical protein	Extracellular	−0.61	1.12	NS	NS
SSA_0334	I	Diphosphomevalonate decarboxylase, putative mvaD	Cytoplasmic	−0.49	0.85	NS	NS
SSA_0335	I	Phosphomevalonate kinase, putative mvaK2	Cytoplasmic	−0.44	0.82	NS	NS
SSA_0336	C	Isopentenyl-diphosphate delta-isomerase, putative	Cytoplasmic	−0.48	0.96	0.69	NS
SSA_0385	R	ABC transporter, glycine-betaine/proline permease protein, putative opuAb	CytoplasmicMembrane	−0.62	0.91	NS	NS
SSA_0386	R	Glycine-betaine ABC transporter, ATPase component, putative opuAa	CytoplasmicMembrane	−0.67	NS	NS	0.97
SSA_0387	P	Transcriptional regulator, GntR family, putative	Cytoplasmic	−0.51	1.21	NS	NS
SSA_0612	L	Rgg protein, putative	Cytoplasmic	−0.39	1.93	1.16	NS
SSA_0613	G	Glucosyltransferase, putative gtfP	Extracellular	−0.42	1.44	0.87	NS
SSA_1359	R	Arginine/histidine ABC transporter, permease component, putative	CytoplasmicMembrane	−0.44	1.41	1.31	NS
SSA_1360	V	Arginine/histidine ABC transporter, ATPase component, putative	CytoplasmicMembrane	−0.44	1.33	1.52	NS
SSA_1361	X	ORFA, transposon ISSsa2	Cytoplasmic	−0.41	1.47	1.26	NS
SSA_1362	X	ORFB, transposon ISSsa2	Unknown	−0.47	1.87	1.64	NS
SSA_1367	P	Hypothetical protein	Cytoplasmic	−0.48	2.22	1.74	NS
SSA_1819	J	Valyl-tRNA synthetase, putative valS	Cytoplasmic	−0.47	NS	NS	1.23
SSA_1928	I	Acyl-CoA dehydrogenase, putative	Cytoplasmic	−0.48	1.08	1.23	NS

Gene refers to the Ensembl gene ID, COG refers to the cluster of orthologous groups. Localization is the predicted localization of each product, identified using pSORTbv3.0. Correlation with MV number refers to the Pearson’s correlation coefficient for each gene with MV number. Log2 FC SK36 suc/glu O2 lists the log2 fold change of each gene significantly different between sucrose and glucose media, oxic conditions. Log2 FC SK36 suc/glu N2 lists the log2 fold change of each gene significantly different between sucrose and glucose media, anoxic conditions. Log2 FC Pg+Ss/Ss lists the log2 fold change of each gene significantly different between S. sanguinis co-cultured with P. gingivalis, over S. sanguinis. NS = not significant.