Contrasting different similarity measures (All species) - PLOS

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100..90 90..80 80..70 70..60 60..50 50..40 40..30 30..20 20..10. 0. 20000. 40000. 60000. 80000. 100000. 120000. 140000. 160000. Excess max Information.
Contrasting different similarity measures (All species) B: Average Information Content 2.6

160000

6

140000

2.4

140000

120000

5

100000

4.5

80000

4

60000

3.5

2.2

120000

2 1.8

100000

1.6

80000

1.4

60000

1.2

3

40000

2.5

20000

0.8

20000

0

0.6

0

160000

0.24

160000

140000

0.22

140000

2

40000

1

0.35

80000 0.3

60000

0.25

40000

0.2 0.15

120000

0.18 0.16

100000

0.14

80000

0.12

60000

0.1

40000

0.08

20000

0.06

20000

0

0.04

0

0

0

..1

20

0

..2

30

..3

0

..4

40

0

..5

50

0

0

..6

60

70

80000

0.16

60000 40000 20000

Excess Schlicker-like Similarity

100000

# Datapoints

0.2 0.18

0.1

0

0.3

120000

0.08

..7

140000

0.12

80

0.26

0.14

..8

0

F: Schlicker-like Similarity 160000

0.22

90

.9

0.

10

0

0

..1

20

..2

30 0

0

..3

..4

40

50 0

..5

0

..6

60

70 0

0

..7

80

..8

90 0

.9

0.

10

E: Maryland-Bridge Similarity 0.28 0.24

# Datapoints

100000

0.2

0

160000 140000

0.25

120000 100000

0.2

80000 0.15

60000

# Datapoints

0.4

# Datapoints

120000

Excess avg Similarity

D: Average Lin Similarity

0.45 Excess max Similarity

0

0

..1

20

0

..2

30

0

..3

40

0

..4

50

0

..5

60

0

..6

70

0

..7

80

0

0

.9

..8

90

0.

10

..1

20 0

..2

30 0

..3

40 0

..4

50 0

..5

60 0

..6

70 0

..7

80

0

0

.9

..8

90

0.

10

C: Maximum Lin Similarity 0.5

Excess Maryland-bridge Similarity

# Datapoints

5.5

Excess avg Information

160000

# Datapoints

Excess max Information

A: Maximum Information Content 6.5

40000

0.1

20000 0.05

0

0 ..1 20

0 ..2 30 0 ..3 40

0 ..4 50 0 ..5 60

0 ..6 70 0 ..7 80

0 ..8 90 0 .9 0. 10

0 ..1 20

0 ..2 30 0 ..3 40

0 ..4 50 0 ..5 60

0 ..6 70 0 ..7 80

0 ..8 90 0 .9 0. 10

Percent Identity

Percent Identity

160000 140000

0.25

120000 100000

0.2

80000 0.15

60000 40000

0.1

20000 0.05

0

0

0

..1

20

0

..2

30

0

..3

..4

40

0

..5

50

0

0

..6

60

70

0

..7

80

0

Feb 14

..8

1:1 orthologs Other orthologs

90

.9 0.

10

Inparalogs Within-spec. outparalogs Between-spec. outparalogs

# Datapoints

Excess Schlicker-exact Similarity

G: Exact Schlicker Similarity 0.3

Percent Identity

Supplementary Figure 10: Different measures of GO term similarity among various types of homologs. The six figures are A) maximum sim , B) average sim , C) maximum sim and D) average sim , E) Maryland-bridge term overlap measure, F) sim (giving same weight to annotation) and G) sim as originally defined in [Schlicker et. al (2006) A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics 7] (giving same weight to each gene product). All similarities are measured from the gene pair s from all 13 analyzed genomes with GO annotations backed by experimental evidence without common authors.