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.