TABLE 4.

Abundance of HSV transcripts at 6 h p.i. in cells infected with the 27lacZ mutant^a

Probe set	27lacZ		KOS		Mutant vs KOS rankb	Probe set	27lacZ		KOS		Mutant vs KOS rank
	Signal	Rank (P)	Signal	Rank			Signal	Rank	Signal	Rank
R.A	784	0.0576	2,420	0.0062	0.0000c	U.35	1,099	0.0001	5,026	0.0000	0.0000
R.O	6,855	0.0000	6,588	0.0000	0.8285	U.36	557	0.9017	3,232	0.0000	0.0001
R.C	473	0.8994	1,296	0.3714	0.0576	U.37	777	0.0187	3,184	0.0000	0.0000
R.D	458	0.9664	1,792	0.2447	0.0568	U.38	4,343	0.0000	6,559	0.0000	0.1080
R.E	1,014	0.0545	1,787	0.0000	0.1264	U.39	7,952	0.0000	9,303	0.0000	0.5991
U.1	4,423	0.0000	7,911	0.0000	0.0340	U.41	706	0.2629	3,255	0.0000	0.0007
U.1X	600	0.6425	1,765	0.0072	0.0452	U.42	710	0.0027	5,913	0.0000	0.0000
U.3	735	0.2103	4,675	0.0000	0.0000	U.43	723	0.2887	1,974	0.0000	0.0002
U.4	971	0.0014	6,005	0.0000	0.0000	U.44	1,512	0.0011	5,744	0.0000	0.0000
U.6	632	0.4950	6,767	0.0000	0.0000	U.46	964	0.0000	4,642	0.0000	0.0000
U.8	601	0.1233	4,505	0.0000	0.0000	U.48	909	0.0004	8,040	0.0000	0.0000
U.10	1,450	0.0000	4,749	0.0000	0.0000	U.49	991	0.0011	5,831	0.0000	0.0000
U.12	627	0.6874	1,336	0.0632	0.0000	U.50	1,407	0.0000	7,546	0.0000	0.0000
U.15	726	0.2105	2,716	0.0000	0.0004	U.51	560	0.8286	3,750	0.0000	0.0000
U.16	389	0.2914	2,054	0.0000	0.0000	U.52	628	0.8284	1,731	0.0000	0.0000
U.18	367	0.1240	4,042	0.0000	0.0000	U.54	676	0.2346	3,561	0.0000	0.0000
U.19X	435	0.4021	9,223	0.0000	0.0000	U.55	574	0.4009	2,437	0.0000	0.0000
U.21	353	0.2004	1,801	0.0000	0.0000	U.56	505	0.3837	1,455	0.0039	0.0000
U.22	421	0.5772	2,767	0.0000	0.0001	R.Fd	663	1.0000	843	0.4187	0.3183
U.23	1,984	0.0156	6,349	0.0000	0.0000	R.4	8,205	0.0000	2,930	0.0000	0.0000
U.24	1,043	0.0218	3,919	0.0000	0.0014	S.1	17,194	0.0000	15,490	0.0000	0.8045
U.25	373	0.2769	3,586	0.0000	0.0000	S.2	650	0.7100	4,664	0.0000	0.0000
U.27	2,098	0.0345	6,367	0.0000	0.0030	S.3	1,166	0.0103	5,010	0.0000	0.0000
U.29	3,030	0.0000	3,729	0.0000	0.9753	S.5	2,287	0.0000	9,329	0.0000	0.0002
U.30	1,812	0.0000	1,051	0.0395	0.6198	S.8	3,623	0.0000	9,464	0.0000	0.0761
U.31	2,211	0.0000	3,616	0.0000	0.0010	S.12	6,451	0.0000	8,189	0.0000	0.7568

^aSignal intensities were determined by calculating the median of background-subtracted values for three independent experiments based on 9 or 18 replicates. P values reported with corresponding median values (Rank) were determined by ranking the replicate values for each sequence (n = 9 or 18) from both mock- and HSV-infected cells. The null hypothesis, that mock and HSV groups are identical, was tested for the ranked values instead of the background adjusted values by using Student's t test with two-tail distribution and assuming unequal variance. This procedure of applying Student's t test to the rank of the signals instead the signal values is an approximation to the nonparametric Mann-Whitney rank test (16). Boldface entries are comparable or increased in 27lacZ (an insertion mutant expressing a chimeric transcript [40, 49, 52]) infection compared to wt KOS infection. 

^bThe null hypothesis is that the mutant (27lacZ) and wt signals are the same. 

^cSignal too low under conditions used for a meaningful conclusion. 

^dP < 0.0001.