Table 1

Benchmarking scores of ortholog identification methods

Method

Direct conservation of function

Pairwise conservation of function

Overall score


Co-expression

Equal InterPro accession number

Conservation of co-expression

Conservation of gene order

Conservation of protein-protein interaction


Hs-Mm

BBH

1.28E+03 (3)

9.49E+03 (6)

2.59E+03 (4)

5.42E+03 (1)

3.18E+02 (1)

5.42E+16 (2)

INP

1.49E+03 (2)

1.13E+04 (5)

2.48E+03 (5)

4.26E+03 (3)

3.13E+02 (2)

5.57E+16 (1)

KOG

4.73E+02 (6)

1.60E+04 (2)

3.08E+03 (3)

1.42E+01 (6)

1.09E+00 (6)

3.61E+11 (6)

MCL

1.66E+03 (1)

1.20E+04 (4)

2.41E+03 (6)

4.56E+03 (2)

2.34E+02 (3)

5.10E+16 (3)

PGT

1.05E+03 (4)

1.53E+04 (3)

4.63E+03 (1)

1.73E+02 (4)

1.21E+02 (4)

1.56E+15 (4)

Z1H

9.29E+02 (5)

1.72E+04 (1)

3.93E+03 (2)

3.75E+01 (5)

3.17E+01 (5)

7.46E+13 (5)

Hs-Ce

BBH

2.25E+03 (5)

3.62E+03 (6)

1.16E+02 (6)

0.00E+00 (6)

5.29E+01 (1)

5.00E+10 (6)

INP

3.02E+03 (3)

5.67E+03 (3)

2.17E+02 (4)

2.79E+02 (1)

7.62E+00 (4)

7.90E+12 (1)

KOG

4.20E+03 (1)

9.51E+03 (1)

6.14E+02 (1)

2.64E+01 (5)

1.17E+00 (6)

7.58E+11 (5)

MCL

2.50E+03 (4)

5.01E+03 (4)

1.76E+02 (5)

2.95E+01 (4)

2.94E+01 (2)

1.91E+12 (2)

PGT

3.89E+03 (2)

9.26E+03 (2)

3.84E+02 (2)

5.36E+01 (2)

1.65E+00 (5)

1.22E+12 (4)

Z1H

2.00E+03 (6)

4.74E+03 (5)

2.97E+02 (3)

4.20E+01 (3)

1.07E+01 (3)

1.27E+12 (3)


Ce, Caenorhabditis elegans; Hs, Homo sapiens; Mm, Mus musculus.

Hulsen et al. Genome Biology 2006 7:R31   doi:10.1186/gb-2006-7-4-r31

Open Data