To test the performance of P2TF, a
variety of approaches were taken. P2TF data were compared to different analyses
available in the literature generated using other search methods. We used these
studies as reference sets and calculated sensitivity and specificity to assess
the efficiency of the P2TF analysis
Species |
Reference TFs |
P2TF TFs |
Sensitivity (%) |
Specificity (%) |
Reference |
Bacillus subtilis
168 |
237 |
281 |
91.6 |
98.4 |
Moreno-Campuzano
et al., 2006 |
Lactobacillus
acidophilus NCFM |
93 |
107 |
93.5 |
98.9 |
Wilson et al., 2008 |
Stenotrophomonas maltophilia
R551-3 |
262 |
292 |
93.9 |
98.8 |
Wilson et al., 2008 |
Corynebacterium efficiens
YS-314 |
103 |
150 |
97.1 |
98.3 |
Brune et al.,
2005 |
Parameters calculation
Sensitivity =
TP/TP+FN
Specificity =
TN/TN+FP
TP. True positive, TN. True
negative, FP. False positive,
FN. False negative
References
Brune,I. et al. (2005) The individual
and common repertoire of
DNA-binding transcriptional
regulators of Corynebacterium
glutamicum, Corynebacterium
efficiens, Corynebacterium diphtheriae and Corynebacterium jeikeium deduced from the complete genome sequences. BMC Genomics, 6, 86.
Moreno-Campuzano,S. et al. (2006) Identification and analysis of DNA-binding
transcription factors in Bacillus subtilis
and other Firmicutes--a genomic approach. BMC Genomics, 7, 147.
Wilson,D. et al. (2008) DBD--taxonomically
broad transcription factor predictions:
new content and functionality. Nucleic
Acids Res, 36, D88-92.