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Table 4 GenSET prediction of known effectors that were included in the testing set. The number of known effector (and percentage) in the top 40 proteins candidates and the overall prediction by GenSET are shown (see Additional file 3 for all top 40 proteins predicted to be T3SS effectors)

From: Computational approach to predict species-specific type III secretion system (T3SS) effectors using single and multiple genomes

GenSET Organism Unfiltered set Filtered set
Top 40 Overallc Top 40 Overall
Phase 1 E. coli 5/6b
(83.3%)
5/6
(83.3%)
4/6
(66.7%)
5/6
(83.3%)
P. syringae 16/30
(53.3%)
16/30
(53.3%)
13/30
(43.3%)
13/30
(43.3%)
S. dysenteriae 5/9
(55.6%)
8/9
(88.9%)
5/9
(55.6%)
5/9
(55.6%)
S. Typhimurium
(SPI-2)
8/9
(88.9%)
8/9
(88.9%)
6/9
(66.6%)
6/9
(66.6%)
Phase 1 Averagea All organisms 70.3% 78.6% 58.1% 62.2%
Phase 2 E. coli 14/21
(66.7%)
19/21 (90.5%) 12/21 (57.1%) 16/21 (76.2%)
Y. pestis 2/8
(25%)
2/8
(25%)
0/8
(0%)
0/8
(0%)
P. syringae 20/51 (39.2%) 36/51 (70.6%) 20/51 (39.2%) 32/51 (62.7%)
S. fredii 4/9
(44.4%)
4/9
(44.4%)
0/9
(0%)
0/9
(0%)
Phase 2 Average All organisms 43.8% 57.6% 24.1% 34.7%
  1. aAverage scores were calculated by averaging the unfiltered and filtered percent values of the four organisms
  2. bEffector prediction rates were calculated by the number of effectors in the top 40 positive prediction over the total number of known effectors in the testing set
  3. cOverall denotes all confirmed effectors proteins that were predicted to be effectors with true probabilities ≥ 0.5