*3.4. Gene Categories Modulated in AFAT*

The differentially regulated genes in AFAT vs. WT trophozoites were classified, according to the protein class they encode, using PANTHER. The categories for functional classification of genes upregulated in AFAT are shown in Figure 2A. The most abundant classes are the gene-encoded protein-binding activity modulator (PC00095), such as AIG1-type G domain-containing protein (EHI\_176590); metabolite interconversion enzyme (PC00262), such as Lecithin:cholesterol acyltransferase (EHI\_065250); protein modifying enzyme (PC00260), such as Leucine rich repeat protein phosphatase 2C domain containing protein (EHI\_178020); and cytoskeletal protein (PC00085), such as F-actin-capping protein subunit beta (EHI\_134490). Of the upregulated genes in AFAT, genes that encode for actin or for actin-binding cytoskeletal proteins, such as actin (EHI\_107290) or EHI\_172960 (Actin-related protein 2/3 complex subunit 3); dehydrogenase (PC00092), such as NAD (FAD)-dependent dehydrogenase (EHI\_099700) or Aldehyde-alcohol dehydrogenase 2

(EHI\_024240); and guanyl-nucleotide exchange factor, such as Ras guanine nucleotide exchange factor (EHI\_023270) or Rho guanine nucleotide exchange factor (EHI\_005910) are significantly enriched according to the PANTHER statistical overrepresentation test (Figure 2B).

The categories for functional classification of genes downregulated in AFAT are shown in Figure 2C. The most abundant class of gene encoded proteins are metabolite interconversion enzyme (PC00262), such as alpha-amylase (EHI\_152880); protein modifying enzyme (PC00260), such as Gal/GalNAc lectin Igl2 (EHI\_183000); and protein-binding activity modulator (PC00095); such as guanylate binding protein (EHI\_175080). Of the downregulated genes in AFAT, no enrichment of a specific biological process was detected according to the PANTHER statistical overrepresentation test.
