Table 2.

Expression Profiles of Putative Plasmodial Proteases

Gene ID	Oligo Microarray (asyn)a	Oligo Microarrayb		Proteomicsc
		T	S	T	M	G	S
PF14_0076	21,915	7595	6935	+	+	+
PF14_0077	6544	6084	3034	+	+	+
PF14_0078	2981	16,185	7152	+	+	+
PF14_0075	20,151	20,979	21,090	+	+	+
PF13_0133	1521	5636	4810
PFC0495w*	454	−	−				+
PF10_0329	76	−	−
PF14_0623	215	−	−
PF14_0281	No oligo
PF08_0108	5561	2478	−				+
PF14_0553	3187	4947	4954				+
PF11_0165	8073	17,895	4771	+
PF11_0162	9302	4559	5676	+		+
PF11_0161	2436	7318	2025	+
PFL2290w*	467	−	−	+		+
PFD0230c	8342	2473	25,913		+
PF11_0174	19,855	36,201	19,570	+	+
PFB0360c	376	−	−
PFB0325c*	179	−	−				+
PFB0330c	2415	2238	5476	+	+
PFB0335c	3428	1695	4803
PFB0340c	28,613	13,254	59,511	+	+
PFB0345c	2273	3115	10,053				+
PFB0350c	4572	−	6320	+		+
PFB0355c	1401	−	−
PFI0135c	3655	2747	3516				+
MAL13P1.310	676	1635	53,119
PF14_0577	1008	−	2060	+
PF11_0177	781	2058	3604				+
PF11_0298	700	−	2514			+
PF13_0289	643	−	1550
PFA0220w	3831	5734	10,100				+
PFD0165w	2208	−	−				+
PFD0680c	894	1696	2387		+
PFE1355c	2840	2251	2414	+	+	+
PFE0835w	2422	−	1831		+
MAL7P1.147	6182	3575	3628	+	+	+	+
PFI0225w	3780	1998	2117				+
PF13_0096	2105	3554	3789
PF14_0145	1826	2428	−				+
PFL1635w	No oligo				+	+
MAL8P1.157	2311	2226	1946				+
MAL6P1.153	No oligo			+	+		+
MAL13P1.56	2788	3250	1588	+	+	+	+
PF10_0058	1765	3672	4309
MAL13P1.184	324	−	−
PFE1155c	3316	3099	2134	+	+	+
PFI1625c	2018	4583	4239		+	+
PF11_0189	4006	4829	3862	+			+
PF11_0226	1002	−	−	+		+	+
PF13_0322	4279	8553	8017	+	+	+	+
PF14_0382	790	−	−
PF14_0439	4828	10,517	4692	+	+		+
PFI1570c	2424	2650	−	+	+	+	+
PF10_0299	1326	2972	1991		+		+
PFE1360c	857	1919	1579	+
MAL8P1.140	3379	2033	−				+
PF10_0150	2880	2103	−	+	+	+
PF14_0327	4130	−	−	+		+	+
PF14_0517	7889	15,722	6630	+	+	+	+
PF11_0203	2440	1695	−
PFL1925w	No oligo			+
PF14_0616	5347	1855	−
MAL8P1.126	1030	−	−
PF14_0067	735	−	−			+
PFE0370c	3384	−	5371		+
T	S	T	M	G	S
PF11_0381	1071	2229	10,369			+
PFE0355c	840	−	4153
PFC0950c	No oligo						+
PFC0310c	3426	2308	3281
PF14_0348	640	2518	2312
PF08_0063	3901	3233	1715	+	+	+	+
PF14_0063	4125	2130	3154
PF11_0175	8264	2856	4534	+	+	+	+
PF14_0147	1023	−	−
PF13_0118	3050	2405	1676
MAL13P1.167	2758	2514	4077
PFE0340c	6507	−	10,279
MAL8P1.16	No oligo
PF14_0716	8791	9053	6476	+	+	+
MAL6P1.88	No oligo				+
PFC0745c	5944	9387	7742	+	+
PF13_0282	7652	7248	5541		+	+
PF07_0112	4279	8258	5730	+	+	+	+
MAL8P1.128	No oligo			+	+	+
MAL13P1.270	1487	6809	5159	+	+	+	+
PFE0915c	3396	5939	5761	+	+
MAL8P1.142	5571	5814	5579	+	+	+
PFA0400c	No oligo			+	+	+	+
PF14_0676	6984	−	−		+
PFI1545c	No oligo				+
PF13_0156	5240	9539	13,684	+	+	+

^aExpression profile of asynchronous culture using Oligo Microarrays. The microarray slide was printed with 6239 70-mers mapped to 4407 predicted open reading frames. Probes were labeled with fluorescent dyes using mRNAs purified from an asynchronous culture as a template (http://derisilab.ucsf.edu/). Briefly, messenger RNAs were purified using oligo T cellulose and reverse transcription was conducted to incorporate aminoallyl dUTP into the cDNAs. The Cy3 and Cy5 NHS esters were then coupled to amine groups of the cDNA, and dye-labeled probes were hybridized with the microarray slides under standard condition (3X SSC, 50% formamide, 0.1% SDS, 10 mg/ml salmon sperm DNA, 68°C). The slide was scanned with a GenePix 4000B (Axon Instrument) at default PMT settings, 100% power. The array data were analyzed initially with GenePixPro software (Axon Instrument), then with global normalization. The expression level is indicated by the mean signal intensity of all corresponding oligomers in triplicates on the microarray slides (MRA-452) obtained from Malaria Research and Reference Resource Center (http://www.malaria.mr4.org/). Ten predicted proteases without corresponding oligomers are highlighted in bold. Two sets of negative controls were included in the DeRisi design: (1) 20 oligomers from yeast intergenic region with the mean intensity 529; (2) 33 P. falciparum genes cloned in the plasmid, including 16 ribosomal proteins, 17 tRNA genes, LSU, Clp, and tufA. Their mean intensity was 598. The percentiles of expression level over all the spots are 297 (30%), 394 (35%), 512 (40%), 646 (45%), and 795 (50%), respectively. The genes that showed signal intensity below the mean of negative controls are highlighted in italic. An asterisk (*) indicates the gene was reported to be expressed in the parasitic life cycle from proteomics data (Florens et al. 2002).

^bExpression profile in the erythrocytic stage using cDNA microarray chip containing 944 elements (317 genes of identiable homology; Ben Mamoun et al. 2001). The average intensities were extracted from PlasmoDB. R, ring. A minus sign (−) indicates signal not detected or below the cut-off (35% percentile over all the spots on the array).

^cExpression profile in the parasite life cycle using MUDPIT proteomics technology (Florens et al. 2002), extracted from PlasmoDB. A plus sign (+) indicates at least one peptide of the protein was detected by Mass Spectrum. T, trophozoites; M, merozoites; G, gametocytes; S, sporozoites.