Fig. 6
Prediction of cis-regulatory motifs from P. falciparum mRNA dynamics. a FIRE analysis prediction of enriched DNA and RNA motifs within the whole genome dynamics data. The profiles of transcription and stabilization are clustered into peak timing during the IDC (columns) predicted enriched motifs arranged into putative functional modules (rows). The yellow color map indicates overrepresentation of a motif in a given cluster; significant overrepresentation (p < 0.05 after Bonferroni correction) is highlighted with red frames. Similarly, the blue color map and blue frames indicate underrepresentation. For each motif, the ApiAP2 trans-factor demonstrated to interact with each predicted motif70 is listed. b The nascent transcription profile of genes identified by FIRE (left panel) or ChIP-seq (right panel71) with the enriched PfAP2-I motif GTGCA are plotted (gray, mean log2 expression value and ±s.e.m.) in comparison to the transcription profile of pfap2-i (red circle). Venn Diagram represents the overlap of genes identified by FIRE (blue) or ChIP-seq (green). c The nascent transcription profile of genes identified by FIRE (left panel) or ChIP-seq (right panel72) with the enriched PfAP2-G2 motif ACAAC are plotted (gray, mean log2 expression value and ± s.e.m.) in comparison to the transcription profile of pfap2-g2 (red). Venn Diagram represents the overlap of genes identified by FIRE (blue) or ChIP-seq (green)
