To test the performance of P2CS, a variety of
approaches were taken. P2CS data were compared to different analyses available
in the literature generated using other search methods. The accuracy of P2CS in
identifying TCS proteins was compared to several studies using manual curation
to detect TCSs. We used these studies as reference sets and calculated
sensitivity, specificity and precision to assess the efficiency of the P2CS
analysis
|
Specie |
Manually defined TCS |
P2CS Predicted TCS |
Sensitivity (%) |
Specificity (%) |
Precision (%) |
Reference |
|
Anaeromyxobacter dehalogenans 2CP-C |
174 |
188 (185+3) |
100 |
99.67 |
92.55 |
Whitworth and Cock, 2008 |
|
Bacillus anthracis str. Ames |
102 (94+8) |
104 (94+10) |
100 |
99.96 |
97.9 |
de Been et al, 2006 |
|
Bacillus anthracis str. Sterne |
102 |
103 |
99.02 |
99.96 |
98.06 |
de Been et al, 2006 |
|
Bacillus cereus ATCC 14579 |
101 (99+2) |
102 (99+3) |
100 |
99.98 |
99.02 |
de Been et al, 2006 |
|
Bacillus cereus ATCC 10987 |
101 (100+1) |
99 (98+1) |
98.02 |
100 |
100 |
de Been et al, 2006 |
|
Bacillus cereus E33L |
107 |
107 |
100 |
100 |
100 |
de Been et al, 2006 |
|
Bacillus subtilis |
70 |
70 |
100 |
100 |
100 |
de Been et al, 2006 |
|
Bacillus thuringiensis serovar
konkukian str. 97-27 |
109 |
109 |
100 |
100 |
100 |
de Been et al, 2006 |
|
Escherichia coli str. K-12 substr.
MG1655 |
62 |
62 (61+1) |
100 |
100 |
100 |
Whitworth and Cock, 2008 |
|
Myxococcus xanthus DK1622 |
278 (276+2) |
283 (281+2) |
99.28 |
99.91 |
97.53 |
Whitworth and Cock, 2008 |
|
Nitrosospira multiformis ATCC 25196
chromosome 1 |
62 |
59 |
93.55 |
99.96 |
98.31 |
Norton et al, 2008 |
|
Pseudomonas syringae pv. syringae
B728a |
142 |
143 |
97.89 |
99.92 |
97.2 |
Lavin et al, 2007 |
|
Pseudomonas syringae pv. tomato str.
DC3000 |
143 (140+3) |
144 (139+5) |
97.2 |
99.92 |
96.53 |
Lavin et al, 2007 |
|
Pseudomonas syringae pv. phaseolicola
1448A |
139 (137+2) |
141 (138+3) |
97.84 |
99.87 |
96.45 |
Lavin et al, 2007 |
|
Sorangium cellulosum So ce56 |
267 |
273 |
98.88 |
99.92 |
96.70 |
Whitworth and Cock, 2008 |
|
Streptomyces coelicolor A3(2) |
164 |
187 |
99.39 |
99.68 |
87.17 |
Hutchings et al, 2004 |
|
Xanthomonas campestris pv. campestris
ATCC 33913 |
106 |
110 |
100 |
99.9 |
96.36 |
Qian et al, 2008 |
|
X. campestris pv. campestris 8004 |
106 |
110 |
100 |
99.9 |
96.36 |
Qian et al, 2008 |
|
X. axonopodis pv. citri 306 |
114 |
120 |
100 |
99.86 |
95 |
Qian et al, 2008 |
|
X. campestris pv. vesicatoria 85-10 |
121 |
126 |
100 |
99.86 |
95 |
Qian et al, 2008 |
|
X. oryzae pv. oryzae KACC10331 |
92 (91+1) |
96 (95+1) |
100 |
99.9 |
95.83 |
Qian et al, 2008 |
|
X. oryzae pv. oryzae MAFF 311018 |
93 |
95 |
100 |
99.95 |
97.89 |
Qian et al, 2008 |
Parameters calculation
Sensitivity = TP/TP+TN
Specificity = TN/TN+FP
Precision = TP/TP+FP
TP. True positive, TN. True negative, FP. False positive, FN. False negative
References
de Been M, Francke C, Moezelaar R, Abee T, Siezen RJ (2006) Comparative analysis of two-component signal transduction systems of Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis. Microbiology 152: 3035-3048.
Hutchings MI, Hoskisson PA, Chandra G, Buttner MJ (2004) Sensing and responding to diverse extracellular signals? Analysis of the sensor kinases and response regulators of Streptomyces coelicolor A3(2). Microbiology 150: 2795-2806.
Lavin JL, Kiil K, Resano O, Ussery DW, Oguiza JA (2007) Comparative genomic analysis of two-component regulatory proteins in Pseudomonas syringae. BMC Genomics 8: 397.
Norton JM, Klotz MG, Stein LY, Arp DJ, Bottomley PJ, Chain PS, Hauser LJ, Land ML, Larimer FW, Shin MW, Starkenburg SR (2008) Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment. Appl Environ Microbiol 74: 3559-3572.
Qian W, Han Z-J, He C (2008) Two-Component Signal Transduction Systems of Xanthomonas spp.: A Lesson from Genomics. Molecular Plant-Microbe Interactions 21: 151-161.
Whitworth DE, Cock PJ (2008) Two-component systems of the myxobacteria: structure, diversity and evolutionary relationships. Microbiology 154: 360-372.