Table V.

Predictions of targeting to different cellular location by eight different prediction programs and experimental confirmation rate

The prediction programs were run against the entire Arabidopsis proteome, and the cross-over sets with the fluorescent protein-derived set (FP), mass spectrometry proteomics-derived set (MS), and Swiss-Prot database-derived set (SP) were determined. The percentages in parentheses are of the predicted proteins as a proportion of the entire experimental sets in each location by each technique; for TargetP, secretory; SubLoc, extracellular; iPSORT, signaling; and Predotar, endoplasmic. Predicted datasets were compared against a combination of experimental sets for ER, Golgi, vacuole, and extracellular.

Predictor, PredictionNo. PredictedNo. Confirmed
FPMSSP
SubLoc, cytosol8,78157 (37%)146 (59%)
WoLF PSORT, cytosol6,29242 (27%)157 (63%)
SubLoc, nucleus11,818173 (54%)150 (41%)382 (69%)
WoLF PSORT, nucleus8,944156 (42%)115 (36%)394 (72%)
PeroxiP, peroxisome1,0816 (13%)8 (29%)5 (55%)
WoLF PSORT, peroxisome3875 (11%)6 (21%)5 (55%)
TargetP, plastid4,42981 (69%)581 (57%)238 (74%)
iPSORT, plastid3,42266 (56%)457 (45%)172 (53%)
Predotar, plastid1,68357 (50%)424 (42%)202 (63%)
WoLF PSORT, plastid6,60874 (63%)569 (56%)226 (70%)
TargetP, secretory5,05849 (23%)270 (30%)287 (62%)
SubLoc, extracellular4,58742 (20%)192 (21%)159 (35%)
iPSORT, signaling4,43846 (22%)258 (28%)267 (58%)
Predotar, ER4,11337 (18%)221 (24%)274 (60%)
WoLF PSORT, ER4284 (10%)12 (28%)
WoLF PSORT, PM3,05929 (35%)175 (33%)84 (72%)
WoLF PSORT, vacuole1,2286 (14%)35 (10%)14 (33%)
TargetP, mitochondrion3,18138 (52%)202 (37%)67 (30%)
SubLoc, mitochondrion3,76525 (34%)192 (35%)56 (25%)
MitoProt II, mitochondrion4,22358 (79%)247 (45%)79 (35%)
iPSORT, mitochondrion4,97545 (62%)242 (44%)72 (32%)
Predotar, mitochondrion1,14234 (45%)150 (27%)60 (26%)
MITOPRED, mitochondrion6,98445 (62%)259 (47%)81 (36%)
WoLF PSORT, mitochondrion1,35118 (25%)137 (25%)56 (25%)