TABLE 2.

Transcript abundance in HeLa cells infected with HSV-1 under various conditions

Transcript, kinetic classb	Remarks (reference[s])c	Abundancea								Rankd
		Cycloheximide RNA		PAA RNA		2-h RNA		8-h RNA		2-h vs 8-h
		Signal	Rank	Signal	Rank	Signal	Rank	Signal	Rank
ICP34.5, L	Neurovirulence (7, 8)	289	0.0081	1,412	0.0158	3,138	0.0002	2,075	0.0002	0.2174
ICP0, IE	trans activator	5,838	0.0000e	4,321	0.0002	8,398	0.0000	8,521	0.0000	0.9556
RHA6, L	1,400 nt 3′ of LAT cap (13)	189	0.0077	1,721	0.0002	775	0.0002	2,017	0.0002	0.0002
ORF-X, L	Low abundance (48)	149	0.0011	1,351	0.1610	736	0.0011	2,945	0.0002	0.0002
ORF-Y, L	Low abundance (48)	152	0.0160	2,021	0.0300	1,171	0.0002	4,347	0.0002	0.0011
UL1/2, L/E	gL/uracil DNA glycosylase (48)	335	0.2817	5,002	0.0003	9,284	0.0000	6,786	0.0000	0.1943
UL3, L	Unknown	381	0.6535	2,109	0.1197	2,393	0.0002	1,488	0.0586	0.0173
UL1X, ?	Antisense to UL1, low abundance (48)	418	0.2691	1,896	0.0001	2,688	0.0000	5,028	0.0001	0.0000
UL4/5, L/E	Unknown/part of helicase-primase complex	408	0.1681	1,821	0.0000	4,192	0.0000	8,868	0.0000	0.0024
UL6/7, L/?	Capsid maturation/unknown	293	0.0030	2,512	0.0000	2,420	0.0000	10,248	0.0000	0.0000
UL8/9, E/E	Part of helicase-primase complex/origin binding	198	0.0648	2,371	0.0000	3,623	0.0000	7,181	0.0000	0.0000
UL10, L	gM	203	0.0171	2,017	0.0098	2,512	0.0001	7,956	0.0004	0.0000
UL11/14, L/E/L/L	UL12 (alkaline exonuclease)/UL13 (protein kinase)	385	0.7781	1,656	0.0000	5,209	0.0003	3,796	0.0000	0.0000
UL15, L	Spliced-DNA packaging	307	0.1029	923	0.0027	2,332	0.0000	5,108	0.0000	0.0006
UL16/17, L/L	Unknown/cleavage and packaging of DNA	235	0.0023	1,043	0.5028	1,827	0.0000	7,272	0.0000	0.0000
UL18/20, L/L/L	VP23 (triplex)/VP5 major capsid protein/membrane associated	173	0.0114	2,497	0.0003	5,373	0.0000	11,972	0.0000	0.0000
UL19/20, L/L	Very weak poly(A) site (9)	266	0.0002	839	0.0059	2,671	0.0000	2,171	0.0038	0.0349
UL21, L	Auxiliary virion maturation function (?)	227	0.0345	1,812	0.0001	3,703	0.0000	5,032	0.0000	0.0119
UL22, L	gH	377	0.6975	2,806	0.0010	9,455	0.0003	5,178	0.0000	0.2581
UL23, E	Thymidine kinase	288	0.1182	1,602	0.4043	6,230	0.0033	3,799	0.0002	0.0000
UL24, L	Unknown regulated poly(A) site (18)	141	0.0440	1,321	0.0048	4,300	0.0034	5,182	0.0056	0.3674
UL25/26/26.5, L/L	Capsid maturation/maturational protease/scaffolding protein	248	0.0005	2,306	0.0002	4,989	0.0001	7,453	0.0000	0.0173
UL27/28, E/L	gB/capsid maturation	278	0.0012	2,286	0.0000	4,270	0.0001	3,607	0.0000	0.6544
UL29, E	Single-stranded DNA binding protein	277	0.0012	2,065	0.0000	3,180	0.0000	2,804	0.0651	0.9111
UL30, E	DNA polymerase	1,029	0.0273	3,823	0.0002	4,308	0.0000	1,523	0.0117	0.0001
UL31/34, L/L/L/L	Nuclear phosphoprotein/capsid maturation/capsid maturation/phosphoprotein	662	0.1221	1,970	0.0000	1,961	0.0062	4,569	0.0005	0.0000
UL35, L	Capsomer tips	392	0.0577	3,162	0.0000	3,249	0.0001	4,075	0.0019	0.1074
UL36, (E)/L	ICP1/2 very large tegument protein (two transcripts, smaller encodes partial ORF)	282	0.0002	1,332	0.0024	1,023	0.0072	6,666	0.0005	0.0000
UL37, E	Tegument phosphoprotein	338	0.0102	2,259	0.0001	1,050	0.0003	4,959	0.0000	0.0000
UL38, L	Efficiency of poly(A) site usage varies with cell type (1, 15)	374	0.0014	1,881	0.0000	518	0.1206	5,818	0.0007	0.0000
UL39/40, E/E	Large and small subunits of ribonucleotide reductase	2,387	0.0002	8,781	0.0001	13,665	0.0000	8,890	0.0000	0.0357
UL41, L	Virion-associated host shutoff protein	341	0.0024	2,022	0.0000	1,111	0.0036	3,217	0.0002	0.0000
UL42/UL43.5, E/L	Part of helicase-primase complex/tegument (57)	256	0.0011	2,990	0.0015	3,699	0.0002	10,491	0.0001	0.0003
UL43, E(?)	Unknown (5)	175	0.0029	1,955	0.0001	470	0.0037	1,453	0.7666	0.0000
UL44/45, L/L	gC/virion associated	422	0.0022	3,647	0.0000	2,033	0.0001	10,352	0.0003	0.0000
UL46/47, L/L	Modulates α-TIF (61)	1,137	0.2912	3,088	0.0000	4,126	0.0000	6,503	0.0000	0.1227
UL48, L	α-TIF	238	0.0477	4,160	0.0000	4,731	0.0000	10,413	0.0000	0.0001
UL49/.49.5, E/L	Tegument protein/unknown	399	0.0787	4,014	0.0006	4,837	0.0003	7,524	0.0000	0.1535
UL50, E	dUTPase	294	0.0011	4,757	0.0000	2,557	0.0010	6,782	0.0000	0.0008
UL51, L	Unknown	149	0.0118	1,661	0.0001	976	0.0096	11,146	0.0000	0.0000
UL52/53, E/L	Helicase-primase complex/gK	255	0.0036	881	0.0040	722	0.1008	1,504	0.0000	0.0000
UL54, IE	RNA transport/inhibition of splicing	12,696	0.0000	9,458	0.0000	11,889	0.0000	6,915	0.0000	0.0000
UL55, E?	Unknown, pathogenesis (3, 38)	102	0.0000	2,184	0.0016	1,000	0.0358	2,225	0.0005	0.0000
UL56, E?	Unknown, pathogenesis (3, 38)	212	0.7744	1,237	0.0052	904	0.0430	1,752	0.0040	0.0736
LAT/(OrfO/P) poly(A) site	Reactivation/modulate ICP0, ICP22/modulate ICP4?) (4, 32, 33, 59)	604	0.1786	1,031	0.0157	475	0.0532	1,499	0.0093	0.0002
ICP4, IE	Broad-range trans activator	6,562	0.0241	3,789	0.0000	4,688	0.0008	7,626	0.0000	0.0172
US1, IE	Host range	21,001	0.0000	17,356	0.0000	18,250	0.0000	12,606	0.0000	0.1714
US2, E?	Unknown	380	0.7366	1,222	0.0094	2,036	0.2530	3,750	0.0001	0.0003
US3/4, E/E?	Protein kinase/gG	364	0.0773	4,625	0.0003	8,562	0.0000	6,639	0.0000	0.0207
US5/6/7, E/E	gJ/gD (entry)/gI (Fc binding)	443	0.1131	7,129	0.0001	12,655	0.0000	8,598	0.0000	0.0344
US8/9, E/E	gE (Fc binding)/unknown	486	0.1692	11,934	0.0000	17,082	0.0000	9,113	0.0000	0.0000
US10/11/12, E/E/IE	Unknown/RNA binding phosphoprotein/α47 (inhibits MHC-I presentation) (60)	13,764	0.0000	7,692	0.0001	14,381	0.0000	10,203	0.0000	0.0636

^aSignal intensities were determined by calculating the median of background-subtracted values for two independent experiments based on 6 or 12 replicates. P values reported with corresponding median values (Rank) were determined by ranking the replicate values for each sequence (n = 6 or 12) from both mock-infected and HSV-infected cells. The null hypothesis (P = 1), 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). 

^bEarly mapping and kinetic data are compiled in reference 45. L, late; IE, immediate early; E, early. 

^cGeneral information concerning genetic functions can be found in reference 37. 

^dThe null hypothesis is that the 2- and 8-h signals are the same. 

^eP < 0.0001.