Winzeler Lab - Supplemental Files for Young et al.

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Additional Files 1. 18 P. falciparum genes used to seed the sporozoite-specific OPI cluster.
Additional Files 2. OPI clusters used for GEMS analysis.
Additional Files 3. Putative cis-regulatory elements discovered by GEMS analysis of promoter regions (1000bp upstream gene start codons). (Download PSSM)
Additional Files 4. Putative cis-regulatory elements discovered by GEMS analysis of gene intron regions. (Download PSSM)
Additional Files 5. Differentially expressed heat shock genes.
Additional Files 6. P. falciparum mitochondrial TCA cycle genes and their life cycle mRNA expression values.

Figure 1. An overview of some of the most biologically interesting putative regulatory elements identified using GEMS and GEMS identification of PfM2.1 from the Sexual Development cluster (GO:GNF0004).
Figure 2. GEMS and MDScan random permutation analyses.
Figure 3. Promoter-derived putative regulatory elements as discovered by OPI cluster.
Figure 4. Alignment of sequences from known and putative rhoptry gene promoter regions containing PfM18.1 and PfM18.1-like motifs.
Figure 5. Results of transient transfection using 1527 base pair promoter region of rap3 cloned upstream luciferase reporter as monitored by qRT-PCR.
Figure 6. Characterization of PfM18.1 binding proteins by EMSA.
Figure 7. Gene-by-gene comparison of expression levels for mixed asexual versus sporozoite stages and mixed asexual parasites versus heat shock treated mixed asexual parasites.

GO	Description	Cluster Size (P.f.)	Cluster Size (P.y.)	Cluster Size (P.b.)	Cluster Size (P.c.)
GO:0020033	antigenic variation	286	108	55	61
GO:0005830	cytosolic ribosome (sensu Eukarya)	89	58	48	44
GO:0007155	cell adhesion	50	14	8	9
GO:0019941	modification-dependent protein catabolism	45	33	21	15
GO:0000502	proteasome complex (sensu Eukarya)	75	61	35	27
GO:0000067	DNA replication and chromosome cycle	96	66	43	31
GO:0005840	ribosome	131	83	61	57
GO:0000278	mitotic cell cycle	333	217	124	107
GO:0005783	endoplasmic reticulum	291	207	121	94
GO:0030260	cell invasion	87	47	23	22
GO:0030894	replisome	100	65	42	31
GO:0006399	tRNA metabolism	324	237	114	126
GO:0006520	amino acid metabolism	398	267	138	147
GO:0006096	glycolysis	97	72	48	42
GO:0006457	protein folding	130	96	50	47
GO:0016052	carbohydrate catabolism	82	58	39	35
GO:GNF0004	Sexual Development	246	145	89	91
GO:0006413	translational initiation	121	85	46	47
GO:0006720	isoprenoid metabolism	45	36	20	16
GO:0020036	Maurer's cleft	243	97	45	47
GO:GNF0006	Sporozoite-specific	37	19	10	10