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Table 1 Strong motif groups identified in the upstream regions of 13 sets of functionally related genes taken from reference [3] (cf., Methods).

From: Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum

aFunctional group

bNo. of genes

cUpstream regions < 2000 nt

dAverage Pearson value

eStrong motif groups

Ring/early trophozoite

    

Transcription machinery

22

15

0.76

G-rich

Cytoplasmic Translation Machinery

132

60

0.83

G-rich, C-rich, TGTG

Glycolytic pathway

11

2

0.70

G-rich

Ribonucleotide synthesis

16

11

0.66

G-rich

Trophozoite/early schizont

    

Deoxynucleotide synthesis

6

1

0.88

no strong motif group identified

DNA replication machinery

32

15

0.81

TGTG, G-rich, CACA, C-rich

TCA cycle

8

3

0.67

G-rich

Proteasome

28

17

0.70

G-rich, CACA, TGTATG

Mitochondrial genes

15

12

0.72

C-rich, TGTG, G-rich

Organellar Translation machinery

33

27

0.74

C-rich, G-rich, TGTG

Schizont

    

Merozoite invasion

55

22

0.75

TGCACA, TGTATG, C-rich, G-rich

Actin myosin motility

10

5

0.83

TGCACA, TGTG, G-rich

Early ring

    

Early ring transcripts

24

2

0.71

no strong motif group identified

  1. a The groups of functionally related genes have been arranged in the order in which they are expressed in the Pf IDC.
  2. b The number of genes (or the number of upstream regions) in each functional group.
  3. c The number of upstream regions in the group that are < 2000 nt in length; for example, in the transcription machinery group, 15 upstream regions out of 22 are < 2000 nt in length.
  4. d The expression profile for each gene in each group has been given in reference [3]. Pearson correlation values were calculated for all pairs of profiles in each group. The average of all pairwise Pearson values in the group is given in the table.
  5. e Strong motif groups (constituted, usually, by motif-sets that are identified by multiple programs and that are related) identified in the upstream regions of each functional group.