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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.