Table 5 Gene Ontology terms enriched in up- and down-regulated genes
From: The genome and transcriptome of the enteric parasite Entamoeba invadens, a model for encystation
GO IDa | GO category name | Genes in genomeb | Genes in subsetc | P-valued |
|---|---|---|---|---|
Up-regulated at 8 h encystation (compared to trophozoite) | ||||
GO:0006030 | Chitin metabolism | 5 | 5 | 1.21 × 10-7 |
GO:0006041 | Glucosamine metabolism | 5 | 5 | 1.21 × 10-7 |
GO:0006807 | Nitrogen compound metabolism | 33 | 7 | 3.33 × 10-4 |
GO:0009308 | Amine metabolism | 27 | 6 | 6.94 × 10-4 |
GO:0005975 | Carbohydrate metabolism | 115 | 11 | 7.92 × 10-3 |
GO:0001522 | Pseudouridine synthesis | 7 | 3 | 2.23 × 10-3 |
GO:0007017 | Microtubule-based process | 13 | 4 | 1.57 × 10-3 |
Up-regulated at 24 h encystation (compared to trophozoite) | ||||
GO:0006030 | Chitin metabolism | 5 | 3 | 4.10 × 10-3 |
GO:0006807 | Nitrogen compound metabolism | 33 | 7 | 1.15 × 10-2 |
GO:0009308 | Amine metabolism | 27 | 6 | 1.52 × 10-2 |
GO:0016311 | Dephosphorylation | 54 | 9 | 2.13 × 10-2 |
GO:0006351 | Transcription, DNA-dependent | 35 | 6 | 4.96 × 10-2 |
GO:0006367 | Transcription initiation from RNA polymerase II promoter | 11 | 3 | 4.78 × 10-2 |
GO:0007017 | Microtubule-based process | 13 | 6 | 2.22 × 10-4 |
GO:0007018 | Microtubule-based movement | 6 | 3 | 7.74 × 10-3 |
Up-regulated at 72 h encystation (compared to trophozoite) | ||||
GO:0009966 | Regulation of signal transduction | 120 | 13 | 7.62 × 10-3 |
GO:0007275 | Development | 10 | 3 | 1.22 × 10-2 |
GO:0040029 | Regulation of gene expression, epigenetic | 8 | 3 | 6.14 × 10-3 |
GO:0006139 | Nucleobase, nucleoside, nucleotide and nucleic acid metabolism | 328 | 24 | 4.39 × 10-2 |
GO:0051056 | Regulation of small GTPase mediated signal transduction | 120 | 13 | 7.62 × 10-3 |
GO:0007017 | Microtubule-based process | 13 | 3 | 2.59 × 10-2 |
Up-regulated at 2 h excystation (compared to 72 h cyst) | ||||
GO:0019318 | Hexose metabolism | 21 | 8 | 9.38 × 10-4 |
GO:0005975 | Carbohydrate metabolism | 115 | 23 | 2.00 × 10-3 |
GO:0044262 | Cellular carbohydrate metabolism | 35 | 10 | 2.79 × 10-3 |
GO:0006096 | Glycolysis | 7 | 4 | 3.51 × 10-3 |
GO:0006007 | Glucose catabolism | 8 | 4 | 6.42 × 10-3 |
GO:0006006 | Glucose metabolism | 17 | 6 | 6.47 × 10-3 |
GO:0006066 | Alcohol metabolism | 28 | 8 | 7.31 × 10-3 |
GO:0051186 | Cofactor metabolism | 54 | 12 | 1.02 × 10-2 |
GO:0016052 | Carbohydrate catabolism | 10 | 4 | 1.62 × 10-2 |
GO:0016226 | Iron-sulfur cluster assembly | 7 | 4 | 3.51 × 10-2 |
GO:0042254 | Ribosome biogenesis and assembly | 18 | 5 | 3.65 × 10-2 |
GO:0008654 | Phospholipid biosynthesis | 14 | 5 | 1.22 × 10-2 |
GO:0046467 | Membrane lipid biosynthesis | 14 | 5 | 1.22 × 10-2 |
GO:0006644 | Phospholipid metabolism | 25 | 7 | 1.34 × 10-2 |
GO:0006497 | Protein lipidation | 10 | 4 | 1.62 × 10-2 |
GO:0006508 | Proteolysis | 138 | 25 | 5.27 × 10-3 |
GO:0006996 | Organelle organization and biogenesis | 112 | 21 | 6.85 × 10-3 |
GO:0006800 | Oxygen and reactive oxygen species metabolism | 5 | 3 | 1.04 × 10-2 |
Up-regulated at 8 h excystation (compared to 72 h cyst) | ||||
GO:0006066 | Alcohol metabolism | 28 | 8 | 1.26 × 10-2 |
GO:0005975 | Carbohydrate metabolism | 115 | 22 | 1.30 × 10-2 |
GO:0019752 | Carboxylic acid metabolism | 26 | 8 | 7.82 × 10-3 |
GO:0009059 | Macromolecule biosynthesis | 202 | 34 | 1.72 × 10-2 |
GO:0006260 | DNA replication | 56 | 12 | 2.65 × 10-2 |
GO:0006139 | Nucleobase, nucleoside, nucleotide and nucleic acid metabolism | 328 | 50 | 2.69 × 10-2 |
GO:0006259 | DNA metabolism | 144 | 25 | 2.71 × 10-2 |
GO:0016568 | Chromatin modification | 11 | 4 | 3.17 × 10-2 |
GO:0006629 | Lipid metabolism | 71 | 19 | 3.61 × 10-4 |
GO:0008610 | Lipid biosynthesis | 21 | 7 | 7.88 × 10-3 |
GO:0044255 | Cellular lipid metabolism | 38 | 10 | 1.02 × 10-2 |
GO:0008654 | Phospholipid biosynthesis | 14 | 5 | 1.78 × 10-2 |
GO:0006644 | Phospholipid metabolism | 25 | 7 | 2.15 × 10-2 |
GO:0006497 | Protein lipidation | 10 | 4 | 2.22 × 10-2 |
GO:0006508 | Proteolysis | 138 | 25 | 1.65 × 10-2 |
GO:0006996 | Organelle organization and biogenesis | 112 | 21 | 1.87 × 10-2 |
Down-regulated at 8 h encystation (compared to trophozoite) | ||||
GO:0009309 | Amine biosynthesis | 10 | 3 | 1.38 × 10-3 |
GO:0006519 | Amino acid and derivative metabolism | 23 | 4 | 1.86 × 10-3 |
GO:0005975 | Carbohydrate metabolism | 115 | 8 | 5.37 × 10-3 |
GO:0019752 | Carboxylic acid metabolism | 26 | 3 | 2.27 × 10-2 |
GO:0051186 | Cofactor metabolism | 54 | 4 | 3.81 × 10-2 |
GO:0016226 | Iron-sulfur cluster assembly | 7 | 4 | 9.80 × 10-6 |
GO:0050896 | Response to stimulus | 46 | 4 | 3.14 × 10-2 |
GO:0006323 | DNA packaging | 39 | 4 | 1.81 × 10-2 |
GO:0051276 | Chromosome organization and biogenesis | 43 | 4 | 2.52 × 10-2 |
GO:0006259 | DNA metabolism | 144 | 8 | 3.36 × 10-2 |
GO:0046467 | Membrane lipid biosynthesis | 14 | 3 | 3.90 × 10-3 |
GO:0006644 | Phospholipid metabolism | 25 | 3 | 2.04 × 10-2 |
GO:0006497 | Protein lipidation | 10 | 3 | 1.38 × 10-3 |
Down-regulated at 24 h encystation (compared to trophozoite) | ||||
GO:0005975 | Carbohydrate metabolism | 115 | 7 | 2.99 × 10-2 |
GO:0050896 | Response to stimulus | 46 | 4 | 3.14 × 10-2 |
GO:0006323 | DNA packaging | 39 | 4 | 1.81 × 10-2 |
GO:0051276 | Chromosome organization and biogenesis | 43 | 4 | 2.52 × 10-2 |
GO:0006259 | DNA metabolism | 144 | 8 | 3.36 × 10-2 |
GO:0031497 | Chromatin assembly | 30 | 3 | 4.27 × 10-2 |
GO:0006461 | Protein complex assembly | 31 | 3 | 4.64 × 10-2 |
Down-regulated at 72 h encystation (compared to trophozoite) | ||||
GO:0006096 | Glycolysis | 7 | 5 | 2.22 × 10-4 |
GO:0019320 | Hexose catabolism | 8 | 5 | 5.42 × 10-4 |
GO:0046365 | Monosaccharide catabolism | 8 | 5 | 5.42 × 10-4 |
GO:0006007 | Glucose catabolism | 8 | 5 | 5.42 × 10-4 |
GO:0005996 | Monosaccharide metabolism | 22 | 8 | 1.19 × 10-3 |
GO:0005975 | Carbohydrate metabolism | 115 | 23 | 1.58 × 10-3 |
GO:0006092 | Main pathways of carbohydrate metabolism | 12 | 5 | 5.35 × 10-3 |
GO:0016052 | Carbohydrate catabolism | 10 | 5 | 2.04 × 10-3 |
GO:0016226 | Iron-sulfur cluster assembly | 7 | 4 | 3.28 × 10-3 |
GO:0031163 | Metallo-sulfur cluster assembly | 7 | 4 | 3.28 × 10-3 |
GO:0006629 | Lipid metabolism | 71 | 15 | 5.95 × 10-3 |
GO:0051258 | Protein polymerization | 4 | 3 | 4.29 × 10-3 |
GO:0030036 | Actin cytoskeleton organization and biogenesis | 7 | 4 | 3.28 × 10-3 |
GO:0030041 | Actin filament polymerization | 4 | 3 | 4.29 × 10-3 |
GO:0008154 | Actin polymerization and/or depolymerization | 4 | 3 | 4.29 × 10-3 |
GO:0016043 | Cell organization and biogenesis | 306 | 51 | 3.70 × 10-4 |
GO:0006996 | Organelle organization and biogenesis | 112 | 21 | 5.58 × 10-3 |
GO:0006800 | Oxygen and reactive oxygen species metabolism | 5 | 4 | 5.58 × 10-4 |
GO:0006801 | Superoxide metabolism | 5 | 4 | 5.58 × 10-4 |
Down-regulated at 2 h excystation (compared to 72 h cyst) | ||||
GO:0007154 | Cell communication | 566 | 23 | 3.73 × 10-2 |
GO:0016043 | Cell organization and biogenesis | 306 | 14 | 4.47 × 10-2 |
Down-regulated at 8 h excystation (compared to 72 h cyst) | ||||
GO:0008643 | Carbohydrate transport | 5 | 3 | 3.56 × 10-3 |
GO:0044249 | Cellular biosynthesis | 276 | 51 | 1.18 × 10-10 |
GO:0006412 | Protein biosynthesis | 194 | 44 | 2.14 × 10-12 |
GO:0006414 | Translational elongation | 11 | 3 | 4.21 × 10-2 |
GO:0051276 | Chromosome organization and biogenesis | 43 | 9 | 3.42 × 10-3 |
GO:0006323 | DNA packaging | 39 | 8 | 6.49 × 10-3 |
GO:0031497 | Chromatin assembly | 30 | 6 | 2.01 × 10-2 |
GO:0006334 | Nucleosome assembly | 23 | 6 | 5.27 × 10-3 |
GO:0006461 | Protein complex assembly | 31 | 7 | 6.20 × 10-3 |
GO:0016043 | Cell organization and biogenesis | 306 | 32 | 2.40 × 10-2 |
GO:0006996 | Organelle organization and biogenesis | 112 | 14 | 3.41 × 10-2 |