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. Author manuscript; available in PMC: 2012 Dec 7.
Published in final edited form as: J Theor Biol. 2011 Aug 27;290:27–36. doi: 10.1016/j.jtbi.2011.08.009

Table 1. Rat liver (in vivo) and human liver cell (in vitro) microarray datasets were used for computational model derivation and evaluation.

Six previously-published microarray sets from four in vivo and two in vitro hepatocellular toxicity experiments were used to construct and validate our prediction model. Four microarray data sets of hepatology Rat1, Human1, and Human2 were from the NCBI GEO database (http://www.ncbi.nlm.nih.gov/geo). Two additional in vivo microarray data sets, Rat2 and Rat3, were obtained from the public web portal of the National Institute of Environmental Health Science (NIEHS, http://cebs.niehs.nih.gov). Rat1 set was chosen and used for our multi-gene model development. Human1 set was used to identify our COXEN genes which showed concordant gene expression networks between in vitro human liver cells and in vivo rat liver cells. The other four sets---Rat2, Rat3, Rat4, and Human2 were used only for our independent evaluation of the hepatocellular toxicity prediction model.

Data Set Sample Species Study usage Sourcea ID Array Platform Samples Drug
Rat1 Rat liver (in vivo) Training GEO GSE5509 Affymetrix Rat 230 2.0 39 6
Human1 Human HepG2 (in vitro) COXEN & Test GEO GSE6907 Affymetrix Human HG-Focus 30 9
Rat2 Rat Liver (in vivo) Test NIEHS 839186700 Affymetrix Rat 230 2.0 34 1
Rat3 Rat Liver (in vivo) Test NIEHS 839173713 Affymetrix Rat 230 2.0 48 1
Rat4 Rat Liver (in vivo) Test GEO GSE8251 GE 990 147
Healthcare/AmershamCodeLi
nkUniSet Rat I
Human2 Human primary Test GEO GSE10410 Affymetrix HG U133 Plus 2.0 37 3
hepatocyte (in vitro)