Additional Files
Additional File 1. 18 P. falciparum genes used to seed the sporozoite-specific OPI cluster.
Additional File 2. OPI clusters used for GEMS analysis.
Additional File 3. Putative cis-regulatory elements discovered by GEMS analysis of promoter regions (1000bp upstream gene start codons). (Download PSSM)
Additional File 4. Putative cis-regulatory elements discovered by GEMS analysis of gene intron regions. (Download PSSM)
Additional File 5. Differentially expressed heat shock genes.
Additional File 6. P. falciparum mitochondrial TCA cycle genes and their life cycle mRNA expression values.
Figures
Figure 1. An overview of some of the most biologically interesting putative regulatory elements identified using GEMS
Figure 2. GEMS identification of PfM2.1 from the Sexual Development cluster (GO:GNF0004)
Figure 3. GEMS and MDScan random permutation analyses
Figure 4. Promoter-derived putative regulatory elements as discovered by OPI cluster
Figure 5. Alignment of sequences from known and putative rhoptry gene promoter regions containing PfM18.1 and PfM18.1-like motifs.
Figure 6. Results of transient transfection using 1527 base pair promoter region of rap3 cloned upstream luciferase reporter as monitored by qRT-PCR.
Figure 7. Characterization of PfM18.1 binding proteins by EMSA.
Figure 8. Gene-by-gene comparison of expression levels for mixed asexual versus sporozoite stages and mixed asexual parasites versus heat shock treated mixed asexual parasites.
Motif Analysis of GO:GNF0004 Cluster Using MDScan and MEME
MDScan Analysis: commands used and summary results (Download all input and result files)
MEME Analysis: commands used and summary results (Download all input and result files)
Additional GEMS Results
Promoter-derived putative regulatory elements for heat shock genes (2kb promoter region).
Intron-derived putative regulatory elements.
Heat Shock CEL Files
PFDP05120601 - control, PFDP05120602 - heat shock
Search a Gene
Top 20 Promoter-derived Motif Candidates for 21 OPI Clusters
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
Total Gene Set (P.f.) 3046 Total Gene Set (P.y.) 1764 Total Gene Set (P.b.) 961 Total Gene Set (P.c.) 903 Expression Profile 