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Table 3 Enriched gained and lost Gene Ontology terms along path from Unikonta to Mammalia

From: Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires

  Enriched gained GO terms P-value Enriched lost GO terms P-value
Unikonta Protein import into peroxisome matrix, docking 9.5E-3   
  cAMP catabolic process 1.9E-2   
  Organelle organization* 2.6E-2   
Opisthokonta Regulation of primary metabolic process 1.3E-2 Protein-heme linkage 5.2E-3
    Asparagine biosynthetic process 1.0E-2
Holozoa (Metazoa and Choanoflagellata) Cell-cell signaling 2.2E-3 Xylan catabolic process 1.6E-5
  Cell surface receptor linked signal transduction 9.2E-3 Carbohydrate metabolic process 3.1E-4
Metazoa Regulation of transcription, DNA-dependent 1.2E-7 Aromatic amino acid family biosynthetic process, prephenate pathway 1.1E-4
    Histidine biosynthetic process 2.3E-3
  Cell-matrix adhesion 4.0E-4 Monosaccharide metabolic process* 6.9E-3
Eumetazoa (Bilaterian Apoptosis 3.1E-4 Protein folding 1.7E-3
and Cnidaria) Peptide cross-linking 4.7E-4 Transcription initiation 3.8E-3
Bilateria Mitochondrial electron transport, NADH to ubiquinone 8.3E-6 Branched chain family amino acid biosynthetic process 3.3E-4
    Histidine biosynthetic process 2.3E-3
  Wnt receptor signaling pathway 2.7E-4 Water-soluble vitamin biosynthetic process* 5.0E-3
Deuterostomia Protein transport 8.2E-2 Cellular amino acid biosynthetic process 7.0E-4
    Phosphoenolpyruvate-dependent sugar phosphotransferase system 3.2E-3
Chordata Lipid catabolic process 3.2E-3 Proteolysis 2.1E-2
  Activation of MAPKK activity 6.7E-3   
Urochordata and Vertebrata Antigen processing and presentation 5.5E-3 Folic acid and derivative metabolic process 2.3E-3
  Protein amino acid phosphorylation 1.8E-2 Oligosaccharide biosynthetic process 3.0E-3
Vertebrata Immune response 4.4E-11 DNA topological change 2.0E-3
  G-protein coupled receptor protein signaling pathway 1.6E-5 Carbohydrate metabolic process 3.1E-3
Tetrapoda Regulation of growth 1.3E-2 Valyl-tRNA aminoacylation 4.3E-3
  Synaptic transmission 2.0E-2 Response to water 8.6E-3
Amniota Immune response 1.8E-3 Regulation of transcription, DNA-dependent 9.2E-8
    Riboflavin biosynthetic process 1.0E-3
  Defense response 2.0E-3 Thiamin biosynthetic process* 1.8E-3
Mammalia Hemopoiesis 2.8E-3 Aromatic amino acid family biosynthetic process 1.1E-2
  Reciprocal meiotic recombination 8.3E-3   
  1. The two terms with the lowest P-values are shown (calculated by the Ontologizer 2.0 software [63] with the Topology-Elim algorithm [64]), with the exception of the four terms marked by an asterisk, due to the relevance of these terms for this work. Prototypical regulatory terms are in bold text, prototypical metabolic terms are in italics (Additional files 5 and 6 list all gained and lost domains together with their associated GO terms and Additional file 14 summarizes the results of using different parameters in Ontologizer 2.0 software).