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Table 2 Overlap with ortholog reference set

From: Benchmarking ortholog identification methods using functional genomics data

  Method Orthologous pairs Orthologous pairs divided by average proteome size False positives
Hox cluster proteins (Hs, 31 unique proteins; Mm, 35 unique proteins; Hs-Mm, 41 protein pairs) BBH 26 2.03E-03 3
  INP 28 1.87E-03 3
  KOG 30 1.65E-03 456
  MCL 26 1.65E-03 25
  PGT 33 2.00E-03 350
  Z1H 26 1.47E-03 19
Nuclear receptors (Hs, 22 unique proteins; Ce, 18 unique proteins; Hs-Ce, 29 protein pairs) BBH 8 1.40E-03 2
  INP 13 1.77E-03 179
  KOG 20 1.82E-03 2,062
  MCL 13 2.04E-03 4
  PGT 11 1.08E-03 180
  Z1H 8 1.56E-03 8
Hemoglobins (Hs, 4 unique proteins; Mm, 9 unique proteins; Hs-Mm, 9 protein pairs) BBH 2 1.56E-04 2
  INP 6 4.02E-04 8
  KOG 4 2.20E-04 52
  MCL 4 2.54E-04 3
  PGT 4 2.42E-04 23
  Z1H 8 4.53E-04 37
Toll-like receptors (Hs, 10 unique proteins; Ce, 1 unique protein; Hs-Ce, 10 protein pairs) BBH 0 0 0
  INP 0 0 0
  KOG 10 9.12E-04 1
  MCL 0 0 0
  PGT 5 4.89E-04 86
  Z1H 0 0 0
Sm proteins (Hs, 13 unique proteins; Mm, 17 unique proteins; Hs-Mm, 17 protein pairs) BBH 5 3.90E-04 8
  INP 5 3.35E-04 8
  KOG 6 3.29E-04 15
  MCL 4 2.54E-04 10
  PGT 7 4.23E-04 18
  Z1H 5 2.83E-04 4
Sm proteins (Hs, 6 unique proteins; Ce, 6 unique proteins; Hs-Ce, 6 protein pairs) BBH 6 1.05E-03 0
  INP 6 8.19E-04 0
  KOG 4 3.65E-04 1
  MCL 6 9.42E-04 2
  PGT 3 2.93E-04 9
  Z1H 0 0 0
  1. Ce, Caenorhabditis elegans; Hs, Homo sapiens; Mm, Mus musculus.