Database composition can affect the structure-activity relationship prediction.
The percent active (A) and inactive (I) chemicals in a database can directly affect the sensitivity (% active chemicals predicted correctly) and specificity (% inactive chemicals predicted correctly) of structure-activity relationship (SAR) analyses. Subdividing the National Center for Toxicological Research (NCTR) liver cancer database (NCTRlcdb) into various A/I ratios, which varied from 0.2 to 5.5, resulted in sensitivity/specificity ratios that varied from 0.1 to 6.5. As percent active chemicals increased (increasing A/I ratio), the sensitivity rose, the specificity decreased, and the concordance (% total chemicals predicted correctly) remained fairly constant. The numbers of chemicals in the various data sets ranged from 187 to 999 and appeared to have no affect on any of the 3 predictors of sensitivity, specificity, or concordance.
Young
John F
JF
Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079-9502, USA. jyoung@nctr.fda.gov
Tsai
Chen-An
CA
Chen
James J
JJ
Latendresse
John R
JR
Kodell
Ralph L
RL
D000818:Animals; D002273:Carcinogens / Q000633:toxicity*; D016208:Databases, Factual; D005544:Forecasting; D006801:Humans; D008113:Liver Neoplasms / Q000139:chemically induced*; D012680:Sensitivity and Specificity; D013329:Structure-Activity Relationship; D015262:Xenobiotics / Q000633:toxicity*
D002273:Carcinogens; D015262:Xenobiotics