Table 2

Overlap with ortholog reference set

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

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