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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
  1. aSelected GO terms that were significantly enriched (P < 0.05) in genes up- or down-regulated at 8 h, 24 h and 72 h post-encystation, and at 2 h post-excystation. bNumber of genes in a GO category in the whole E. invadens genome. cNumber of genes in a GO category among the subset of regulated genes. dP-value for GO category enrichment.