TABLE 4.

Locations and expression levels of several RNA transcripts within intergenic regions identified by microarray hybridization

GAP region (flanking genes)	Coordinatesa (bp)	Positive probe pairs (position)b	Expression levelc in:						Homologyd
			MM			LB
			Log	Stat	Fold change	Log	Stat	Fold change
68D-R (perR/ygxA)	944257–944854	1–15	480	2,800	0.17	220	130	1.7	B. subtilis ygzB, B. stearothermophilus ORF3663, and B. halodurans BH0952
74-R (yhbF/prkA)	972141–972492	9–19	1,300	4,900	0.26	230	1,200	0.19	B. halodurans BH1024
96-R (yjiC/yjjA)	1293043–1293447	5–15	190	80	2.4	<50	<50	NTe	None
123-F (slp/cad)	1533009–1533588	10–20	<50	7,000	0.007	90	150	0.6	B. stearothermophilus ORF4213
163-2-R (yoaM/yoaN)	2036272–2036634	1–20	370	280	1.3	150	<50	3.0	B. subtilis ynxB and RBS04224
169A-R (xynA/yobD)	2056788–2057011	3–13	260	100	2.6	90	80	1.1	None
172-1-F (yozJ/rapK)	2059904–2060133	1–20	1,200	3,000	0.4	140	<50	2.8	B. subtilis yobB
206A-F (ypjQ/ypiP)	2298343–2298604	10–20	1,200	3,900	0.3	580	290	2.0	None
240-F (yqeN/comEC)	2636363–2636768	9–20	2,600	4,600	0.56	880	110	8.0	B. halodurans BH1336
241-F (yqeG/yqeF)	2646336–2647145	4–20	570	290	2.0	<50	<50	NT	B. subtilis sda and B. halodurans GH1321
342-F (yvcP/yvcN)	3567166–3567559	2–19	200	90	2.2	150	<50	3.0	None

^aCoordinates taken from SubtiList (http://genolist.pasteur.fr/SubtiList). 

^bThat is, the position of probe pairs within each probe set (20 probe pairs per probe set) that generated a positive hybridization signal according to Affymetrix hybridization metrics. 

^cThe average difference values (after normalization) of B. subtilis PY79 grown to exponential or stationary phase in minimal medium (MM) or LB broth (LB). Values were determined from either duplicate (MM) or single (LB) hybridization experiments. Fold change values indicated in boldface were confirmed by RT-PCR. Log, log phase; Stat, stationary phase. 

^dHomology of putative coding regions that correspond to detected RNA transcripts. 

^eNT, no transcript detected.