Fig. 2

Effects of K13 dysregulation on transcriptome. (a) Comparing wild-type and K13 mutant transcript expression at their respective time points shows that the two strains are very similar. Grey dots represent absolute fold changes greater than 2.5. (b) Clustering all of the time-points based on their similarity to the 3D7 reference transcriptome from Derisi shows that from a global perspective the two strains are very similar and the time points have their highest similarities to the expected reference time-points and progression through the erythrocytic cycle is visible in the heatmap. However, at the 6 h time-point the mutant strain shows a stronger similarity to trophozoite time-points compared to the wild-type strain and at 24 h the mutant shows a less dramatic shift towards similarity with earlier time points. (c) Plotting the sample correlations with the 3D7 reference transcriptome from Derisi makes the disruption to the mutant 6 h transcriptome more evident. With the exception of the mutant 6 h they all show that there is a gradual increasing in similarity as the sample time point approaches the equivalent 3D7 time point and then a gradual decrease in similarity as it moves away from the time point. This periodic structure is disrupted in the mutant at 6 h. The sequencing quality of the wild-type and mutant 6 h samples are equivalent (Additional file 1: S1) indicating this disruption cannot be attributed to differences in sequencing quality. This transcriptomic shift is also not attributable to increased sample variation since variation in the 6 h samples is no greater than the variation of the other time point samples (Additional file 1: S5) or to a transposon specific effect (Additional file 1: S6). The arrows are indicating the direction of the transcriptome shifts