TABLE 2.

Abscess-specific increased gene expression

S. intermedius TYG1620 genome annotation			RNA-seq results
			RPKMa			Expression ratio (fold change)
Locus tag identifier	Product	Length (no. of aa)	Early log phase (BHI, 6 h)	Stationary phase (BHI, 24 h)	Subcutaneous abscess	Abscess/BHI, 6 h	Abscess/BHI, 24 h
SITYG_00160	Competence-specific global transcription modulator	157	166.3	139.1	614.4	4.0	3.7
SITYG_01550b	Hypothetical protein	96	57.0	0.0	276.1	5.3	>276.1
SITYG_02340	Hypothetical protein	210	249.0	173.6	1,031.2	4.5	5.0
SITYG_02390	Hypothetical protein	86	79.5	0.0	500.2	6.9	>500.2
SITYG_04050	Hypothetical protein	55	74.1	130.8	836.8	12.3	5.3
SITYG_04300c	Hypothetical protein	42	32.2	170.3	1,556.9	52.7	7.6
SITYG_06280	Hypothetical protein	83	0.0	87.2	318.8	>318.8	3.0
SITYG_07460	Hypothetical protein	42	32.2	0.0	389.2	13.2	>389.2
SITYG_07920	Hypothetical protein	244	28.2	59.8	368.9	14.2	5.1
SITYG_08020	Hypothetical protein	87	0.0	0.0	152.2	>152.2	>152.2
SITYG_08690	Hypothetical protein	57	262.2	0.0	865.7	3.6	>865.7
SITYG_08800	Hypothetical protein	258	165.5	141.4	542.8	3.6	3.2
SITYG_10090	Hypothetical protein	110	99.7	132.0	542.8	5.9	3.4
SITYG_10160	Hypothetical protein	54	0.0	0.0	121.7	>121.7	>121.7
SITYG_11120	Hypothetical protein	143	28.8	50.9	186.0	7.0	3.0
SITYG_12600	Putative membrane protein	187	58.8	272.7	997.1	18.5	3.0
SITYG_15030	Gcn5-related N-acetyltransferase	165	141.6	132.4	665.4	5.1	4.2
SITYG_16520	Hypothetical protein	62	21.9	116.3	531.3	26.4	3.8
SITYG_17490	Hypothetical protein	109	25.1	133.2	486.9	21.1	3.0
SITYG_19180	Hypothetical protein	172	55.9	84.7	483.7	9.4	4.8
SITYG_19530c	Hypothetical protein	40	33.7	178.7	979.7	31.6	4.6
SITYG_19560	Hypothetical protein	40	0.0	0.0	979.7	>979.7	>979.7
SITYG_19770	Hypothetical protein	54	100.6	133.2	1,338.9	14.5	8.4
SITYG_20170	Hypothetical protein	48	56.4	0.0	204.9	4.0	>204.9

^aRPKM, number of reads per kilobase per million.

^bORF located in T7SS (Fig. 2C).

^cPotential candidates for PSMs; see prediction of the secondary structure in Fig. 4F.