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

Additional file 1:

Over-represented upstream motifs identified for the 4 functional groups of genes expressed during the ring to early trophozoite transition. Sets of over-represented motifs identified for each functional group by 3 motif-discovery programs, sequence logos for the sets, grouping of the sets into strong and weak motif groups, and feature maps for each group, are given.

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Additional file 2:

Over-represented upstream motifs identified for the 6 functional groups of genes expressed during the trophozoite to early schizont transition. Strong and weak motif groups identified for each functional group are given.

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Additional file 3:

Over-represented upstream motifs identified for the 2 functional groups of genes expressed during the mid- and late-schizont stages. Strong and weak motif groups identified for each functional group are given.

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Additional file 4:

Over-represented upstream motifs identified for the single functional group of genes expressed during the early ring stage. Over-represented motif sets identified for the functional group are given.

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Additional file 5:

Motif occurrences in the strong motif groups, identified for each of the 13 functional groups of genes, after sorting. These motif occurrences were used to obtain feature maps.

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Additional file 6:

The list of putative regulatory motifs occurring in the upstream regions of the 13 functional groups of genes. The sequence and upstream position of each putative regulatory motif is given.

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Additional file 7:

Feature maps for the strong motif groups identified in the upstream regions of the 13 functional groups of genes. The maps have been obtained after sorting the motifs in each strong motif group.

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Additional file 8:

Statistically validated positionally conserved motifs. Positionally conserved upstream motifs which have been statistically validated by Monte Carlo simulations are listed.

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Additional file 9:

Feature maps showing the occurrence of putative Pf regulatory motifs in ESTs and orthologous sequences. The maps show the distribution of putative Pf regulatory motifs (a) in ESTs retrieved for the gene upstream sequences and (b) in the upstream sequences of orthologous genes from other Plasmodium species.

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Additional file 10:

Positional conservation information for the strong motif groups identified for the 13 functional groups of genes. The table summarizes the positional conservation information for motifs in all functional groups and helps the reader navigate through the Additional files.

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