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Table 1 Results from computational approaches predicting nuclear proteome membership

From: Towards defining the nuclear proteome

Method

NUCPROT proteins classified as 'nuclear'

Accuracy

RIKEN proteome proteins classified as 'nuclear'

CELLO

2,125

78%

9,122 (47%)

pTARGET

1,706

63%

5,953 (30%)

Proteome Analyst

1,803

66%

4,084 (21%)

WoLF PSORT

1,909

70%

7,172 (37%)

MultiLoc

1,561

57%

5,137 (26%)

Yeast homology (E < 10-4)

218

8.0%

2,031 (8.0%)

Yeast homology (E < 10-30)

47

1.7%

691 (3.5%)

Mouse homology

430

16%

766 (3.9%)

Nucleo

857

32%

987 (5.0%)

  1. For the subcellular localization prediction programs, proteins were considered to be incorrectly classified as 'not nuclear' if the method's top-ranked localization call was not 'nucleus' but the protein was in our high-quality dataset; proteins were considered to be correctly classified as 'nuclear' if the method's top-ranked localization call was 'nuclear' and the protein was in our high-quality dataset.