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

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)

GenSET	Organism	Unfiltered set		Filtered set
GenSET	Organism	Top 40	Overall^c	Top 40	Overall
Phase 1	E. coli	5/6^b (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 Average^a	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%

^aAverage scores were calculated by averaging the unfiltered and filtered percent values of the four organisms
^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
^cOverall denotes all confirmed effectors proteins that were predicted to be effectors with true probabilities ≥ 0.5

ISSN: 1471-2164