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Table 1 Summary of genomes in the reference sets

From: Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment

  Bacteria   Eukaryotes  
Profile Architecture Actino Firmicutes Spirochaetes Proteo Others Archaea Metazoans Fungi Plants Apicomplexa Others Number of Genomes
B 3 10 2 17 9 0 0 0 0 0 0 41
BA 3 10 2 17 9 11 0 0 0 0 0 52
BAE1 3 10 2 17 9 11 0 1 1 1 0 55
BAE2 3 10 2 17 9 11 2 1 1 1 0 57
BAE3a 3 10 2 17 9 11 3 2 1 1 1 60
BAE3b 3 10 2 17 9 11 3 2 1 1 1 60
NR 2 9 2 14 7 11 3 2 1 1 1 53
NR-3 1 9 2 12 7 11 3 2 1 1 1 50
NR-8 1 8 2 10 6 10 3 2 1 1 1 45
LA 1 5 2 10 6 10 3 2 1 1 1 42
LAc 2 5 0 7 3 10 3 2 1 1 1 35
BAE4 3 10 2 17 9 11 19 16 1 5 2 95
BAE5 1 1 1 1 3 11 19 16 1 5 2 61
BAE6 1 2 1 3 5 3 2 2 1 1 2 23
AE 0 0 0 0 0 11 19 16 1 5 2 54
E 0 0 0 0 0 0 19 16 1 5 2 43
  1. Notes: B – All 41 bacterial genomes; BA – 41 bacterial and 11 archaeal genomes; BAE1 – BA genomes plus 3 eukaryotic genomes (S. cerevisiae, A. thaliana, P. falciparum); BAE2 – BA genomes plus 5 eukaryotic genomes (D. melanogaster, C. elegans, S. cerevisiae, A. thaliana, and P. falciparum); BAE3a – BA genomes plus 8 eukaryotic genomes (M. musculus, D. melanogaster, C. elegans, S. cerevisiae, S. pombe, D. discoideum, A. thaliana, and P. falcifarum); BAE3b – BA genomes plus 8 eukaryotic genomes (C. familiaris, A. mellifera, C. elegans, C. albicans, S. pombe, D. discoideum, A. thaliana, and P. vivax); NR – BAE3a minus 7 bacterial strains; NR-3 – NR minus 3 bacterial genomes (M. leprae, R. prowazekii, and X. fastidiosa); NR-8 – NR-3 minus 4 bacterial genomes (M. pulmonis, C. trachomatis, Buchnera sp. APS, and P. multocida) and 1 archaeal genome (P. abyssi); LA – NR-8 minus 3 bacterial genomes (S. pyogenes SF370, M. genitalium, and M. pneumoniae); LAc – Set of eukaryotic and archaeal genomes used in LA along with the set of bacterial genomes not included (complementary set) in LA; BAE4 – All 95 genomes under consideration (41 bacteria, 11 archaea, and 43 eukaryotes); BAE5 – All Archaeal and eukaryotic genomes plus a selected set of 7 bacterial genomes; BAE6 – A selected of 23 genomes (12 bacteria, 3 Archaea, and 8 eukaryotes); AE – All Archaeal and eukaryotic genomes; E – All 43 eukaryotic genomes.