Table 3.
A subset of genes down-regulated in 5-AzaC treated E. histolytica HM-1:IMSS parasites as compared to untreated controls.
| Probe set | Baseline expression | Fold-change | p-value | Annotation |
| Potentially virulence associated | ||||
| 2.m00545_at*£ | 4.12 | 0.27 | 0.033 | cysteine proteinase, putative (GO:0006508) |
| 52.m00148_at | 0.96 | 0.46 | 0.018 | lysozyme, putative |
| 1.m00663_at | 6.21 | 0.36 | 0.006 | myosin calcium-binding light chain, putative (GO:0005509) |
| Protein kinases | ||||
| 35.m00259_at | 1.76 | 0.48 | 0.013 | protein kinase, putative (GO:0005524) |
| 67.m00091_x_at£ | 3.42 | 0.37 | 0.033 | protein kinase, putative (GO:0005524) |
| 99.m00190_s_at | 0.39 | 0.46 | 0.040 | protein kinase, putative (GO:0006468) |
| 466.m00033_x_at | 0.51 | 0.47 | 0.003 | protein kinase, putative (GO:0005524) |
| 264.m00068_at | 2.29 | 0.44 | 0.029 | protein kinase, putative (GO:0005524) |
| GTPases | ||||
| 106.m00140_at | 2.39 | 0.48 | 0.025 | Rap Ran GTPase activating protein, putative |
| 2.m00606_x_at | 0.20 | 0.36 | 0.005 | Rab family GTPase (GO:0005524) |
| 226.m00092_at* | 0.34 | 0.44 | 0.008 | Rab family GTPase |
| 30.m00257_at | 4.28 | 0.50 | 0.023 | Rab family GTPase (GO:0005524) |
| 34.m00273_x_at | 3.22 | 0.43 | 0.040 | Rab family GTPase (GO:0005524) |
| 71.m00153_x_at£ | 2.21 | 0.47 | 0.002 | Rho family GTPase (GO:0005525) |
| 8.m00366_s_ata | 1.15 | 0.46 | 0.021 | Rho GTPase activating protein, putative |
| 171.m00089_at | 4.88 | 0.35 | 0.044 | GTPase activating protein, putative (GO:0003924) |
| Genes with decreased expression in E. histolytica (Rahman) compared to E. histolytica (HM-1:IMSS) | ||||
| 108.m00122_at | 32.12 | 0.21 | 0.036 | hypothetical protein |
| 136.m00107_at | 1.20 | 0.38 | 0.030 | hypothetical protein |
| 22.m00298_at | 4.12 | 0.43 | 0.002 | hypothetical protein |
| 297.m00061_at | 5.00 | 0.35 | 0.010 | hypothetical protein |
| 32.m00239_at | 0.93 | 0.46 | 0.039 | N-acetylglucosaminyl transferase, putative |
| 37.m00215_at | 1.90 | 0.46 | 0.035 | hypothetical protein |
| 442.m00023_x_at | 0.82 | 0.44 | 0.006 | hypothetical protein |
| 460.m00024_s_atb | 2.18 | 0.27 | 0.015 | hypothetical protein |
| Genes overlap with day-1 & day-29 significantly up-regulated genes from in vivo mouse model (Gilchrist et al, 2006)£ | ||||
| 15.m00302_at | 4.05 | 0.41 | 0.030 | hypothetical protein |
| 2.m00545_at* | 4.12 | 0.27 | 0.033 | cysteine proteinase, putative (GO:0006508) |
| 67.m00091_x_at | 3.42 | 0.37 | 0.033 | protein kinase, putative (GO:0005524) |
| 71.m00153_x_at | 2.21 | 0.47 | 0.002 | Rho family GTPase (GO:0005525) |
| Miscellaneous | ||||
| 338.m00049_s_atc | 4.30 | 0.42 | 0.020 | LIM domain protein (GO:0008270) |
| 10.m00349_x_at | 4.30 | 0.44 | 0.024 | paxillin, putative (GO:0008270) |
| 35.m00253_at | 1.74 | 0.26 | 0.036 | iron-sulfur flavoprotein, putative (GO:0006118) |
| 646.m00021_s_at | 0.36 | 0.40 | 0.009 | iron-sulfur flavoprotein, putative |
| 90.m00179_at | 1.31 | 0.46 | 0.044 | amino acid transporter, putative (GO:0006865) |
| 139.m00118_at | 3.90 | 0.44 | 0.048 | histone H3, putative (GO:0005634) |
a8.m00366_s_at also represents 58.m00170 (Rho GTPase activating protein, putative)
b460.m00024_s_at also represents 353.m00048 (hypothetical protein) and 353.m00049 (hypothetical protein)
c338.m00049_s_at also represents 321.m00056 (LIM domain protein)
The probe set, baseline expression value in untreated E. histolytica HM-1:IMSS trophozoites, fold change in 5-AzaC treated parasites, p-value, and gene annotation are shown. Genes are clustered according to functional categories. Genes in bold are those for which RT-PCR confirmation was performed. Genes with normalized expression values >0.20 can routinely be detected by RT-PCR. Genes marked by * are those for which bisulfite sequencing was performed. Genes that were significantly upregulated in E. histolytica HM-1:IMSS trophozoites passed through mice are obtained from Gilchrist et al [27] and are indicated by £. For annotations, GO IDs are given where available and are provided within parentheses.