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Table 3 Predictive results obtained by using various similarity definitions for proteins

From: Assessing protein similarity with Gene Ontology and its use in subnuclear localization prediction

Similarity Definition MAX AVG SUM AVG_BestPairs
Compartment MCC (Accuracy %)
PML BODY 0.189 (28.9) 0.153 (34.2) 0.129 (76.3) -0.031 (0.0)
Nuclear Lamina 0.344 (45.5) 0.535 (63.6) 0.455 (45.5) 0.315 (61.8)
Nuclear Splicing Speckles 0.377 (35.7) 0.251 (71.4) 0.289 (33.9) 0.013 (12.5)
Chromatin 0.236 (19.7) 0.218 (16.4) 0.112 (4.9) 0.142 (8.2)
Nucleoplasm 0.272 (29.3) 0.039 (9.3) -0.079 (4.0) 0.118 (6.7)
Nucleolus 0.367 (75.8) 0.431 (44.7) 0.214 (26.0) 0.289 (75.3)
Overall for Single-localization 0.298 (50.8) 0.271 (40.3) 0.187 (27.0) 0.141 (42.9)
Similarity Definition SUM_BestPairs AVG_Match SUM_Match MAX_Match
Compartment MCC (Accuracy %)
PML BODY 0.242 (44.7) 0.187 (34.2) 0.253 (34.2) 0.211 (31.6)
Nuclear Lamina 0.53 (67.3) 0.586 (60.0) 0.578 (63.6) 0.344 (45.5)
Nuclear Splicing Speckles 0.438 (46.4) 0.397 (66.1) 0.607 (62.5) 0.487 (46.4)
Chromatin 0.325 (36.1) 0.467 (45.9) 0.518 (60.7) 0.263 (21.3)
Nucleoplasm 0.284 (36.0) 0.332 (32.0) 0.504 (56.0) 0.298 (32.0)
Nucleolus 0.512 (66.7) 0.615 (72.6) 0.656 (79.0) 0.407 (76.7)
Overall for Single-localization 0.388 (54.6) 0.431 (58.3) 0.519 (66.5) 0.335 (53.2)
  1. (Based on SimLP: The GO term similarity is defined on the longest path shared by two GO terms [22].)