Table 3

Comparison of predicted versus experimentally determined status of proteins

Group

Localization signal/protein domain

Hypothetical proteins

Characterized proteins

Removed proteins

Characterized mitochondrial proteins


I

20

30%

(6 of 20)

65%

(13 of 20)

5%

(1 of 20)

85%

(11 of 13)

II

56

27%

(15 of 56)

64%

(36 of 56)

9%

(5 of 56)

58%

(21 of 36)

III

100

36%

(36 of 100)

53%

(53 of 100)

11%

(11 of 100)

45%

(24 of 53)


2006 dataset

-

25%

(1455 of 5860)

21%

(1215 of 5860)

54%

(3190 of 5860)

6%

(67 of 1215)


Hypothetical proteins from the 2006 dataset sorted into groups depending on the probability of having a mitochondrial N-terminal presequence localization signal. Proteins of Group I, have been predicted by TargetP to belong to reliability class A, indicating the strongest prediction. Proteins of Group II contain proteins belonging to reliability class A and B, while proteins of Group III contain proteins belonging to reliability class A, B and C. All proteins of Group I, II and III have identifiable protein domains according to SMART. The three groups have been compared with all 5860 proteins of the 2006 dataset, and with their respective 2008 annotations, to evaluate whether the proteins have been characterized as being mitochondrial or have been removed.

Desler et al. BMC Bioinformatics 2009 10:289   doi:10.1186/1471-2105-10-289

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