Table 1. T. denticola and P. gingivalis genes differentially expressed during continuous co-culture relative to mono-culture, grouped by COG category.

	*	No. of genes in P. gingivalis	Differentially expressed P. gingivalis genes		No. of genes in T. denticola	Differentially expressed T. denticola genes
	COG		TOTAL	% of COG		TOTAL	% of COG
Information storage and processing	J	117	6	5.1	138	1	0.7
	K	38	2	5.3	62	8	12.9
	L	88	10	11.4	86	2	2.3
Cellular processes and signaling	D	15	0	0.0	15	0	0.0
	V	27	3	11.1	93	5	5.4
	T	27	4	14.8	85	9	10.6
	M	109	2	1.8	101	9	8.9
	N	6	1	16.7	27	0	0.0
	U	15	1	6.7	35	3	8.6
	O	52	7	13.5	55	10	18.2
Metabolism	C	73	1	1.4	61	3	4.9
	G	48	1	2.1	73	4	5.5
	E	73	1	1.4	100	15	15.0
	F	52	1	1.9	45	2	4.4
	H	89	7	7.9	51	3	5.9
	I	33	4	12.1	40	3	7.5
	P	48	3	6.3	104	4	3.8
	Q	7	0	0.0	5	0	0.0
Poorly or not characterized	R	128	8	6.3	188	10	5.3
	S	62	2	3.2	159	13	8.2
	N/A	710	70	9.9	1263	80	6.3
	Total	1817	134	7.4	2786	184	6.6

* One-letter abbreviations for the functional COG categories: J, translation, ribosomal structure and biogenesis; K, transcription; L, replication, recombination and repair; D, cell cycle control, cell division, chromosome partitioning; V, defense mechanisms; T, signal transduction mechanisms; M, cell wall/membrane/envelope biogenesis; N, cell motility; U, intracellular trafficking, secretion, and vesicular transport; O, posttranslational modification, protein turnover, chaperones; C, energy production and conversion; G, carbohydrate transport and metabolism; E, amino acid transport and metabolism; F, nucleotide transport and metabolism; H, coenzyme transport and metabolism; I, lipid transport and metabolism; P, inorganic ion transport and metabolism; Q, secondary metabolites biosynthesis, transport and catabolism; R, general function prediction only; S, function unknown.