Figure 5. After removing the signal of cell cycle progression, we identify a new class of cell-cycle independent variable genes.
(A) P. falciparum genes with >= 50% of their variance attributed to cell-cycle associated latent variable one vary in pseudotime. After removing variation associated with the cell cycle, 56 genes with >= 50% of their variance remained. Highly enriched functional terms associated with the two sets of genes are shown. (B) Here, we show that cell-cycle independent variable transcripts have similar half lives to genes in general during the ring and trophozoite stages. However, during the schizont stage and later, they are significantly longer. The data was derived from (Shock et al., 2007). (C) A conservation score, calculated based on mean amino acid substitution between P. berghei and P. falciparum proteins, was plotted against expression level (scran-l) for each cell-cycle-dependent and each cell-cycle-independent gene in P. falciparum. Density plots show the distributions of each of these parameters, highlighting that cell-cycle-independent genes tend to have higher conservation scores, but similar expression levels.
Figure 5—figure supplement 1. Latent factor analysis of expression variation in cell cycle genes.
