156
D. L. Svoboda et al.
9. Natsoulis G, El Ghaoui L, Lanckriet GR, Tolley AM, Leroy F, Dunlea S, Eynon BP, Pearson
CI, Tugendreich S, Jarnagin K (2005) Classification of a large microarray data set: algorithm
comparison and analysis of drug signatures. Genome Res 15(5):724–736
10. Natsoulis G, Pearson CI, Gollub J, Eynon BP, Ferng J, Nair R, Idury R, Lee MD, Fielden
MR, Brennan RJ, Roter AH, Jarnagin K (2008) The liver pharmacological and xenobiotic gene
response repertoire. Mol Syst Biol 4(1):175
11. AbdulHameed MD, Ippolito DL, Stallings JD, Wallqvist A (2016) Mining kidney toxicogenomic data by using gene co-expression modules. BMC Genom 17(1):790
12. Ippolito DL, AbdulHameed MD, Tawa GJ, Baer CE, Permenter MG, McDyre BC, Dennis
WE, Boyle MH, Hobbs CA, Streicker MA, Snowden BS, Lewis JA, Wallqvist A, Stallings JD
(2016) Gene expression patterns associated with histopathology in toxic liver fibrosis. Toxicol
Sci 149(1):67–88
13. AbdulHameed MD, Tawa GJ, Kumar K, Ippolito DL, Lewis JA, Stallings JD, Wallqvist A
(2014) Systems level analysis and identification of pathways and networks associated with
liver fibrosis. PLoS ONE 9(11):e112193
14. Tawa GJ, AbdulHameed MD, Yu X, Kumar K, Ippolito DL, Lewis JA, Stallings JD, Wallqvist A
(2014) Characterization of chemically induced liver injuries using gene co-expression modules.
PLoS ONE 9(9):e107230
15. Gusenleitner D, Auerbach SS, Melia T, Gomez HF, Sherr DH, Monti S (2014) Genomic models
of short-term exposure accurately predict long-term chemical carcinogenicity and identify
putative mechanisms of action. PLoS ONE 9(7):e102579
16. Adler M, Ramm S, Hafner M, Muhlich JL, Gottwald EM, Weber E, Jaklic A, Ajay AK, Svoboda
D, Auerbach S, Kelly EJ, Himmelfarb J, Vaidya VS (2016) A quantitative approach to screen
for nephrotoxic compounds in vitro. J Am Soc Nephrol 27(4):1015–1028
17. Fielden MR, Brennan R, Gollub J (2007) A gene expression biomarker provides early prediction
and mechanistic assessment of hepatic tumor induction by nongenotoxic chemicals. Toxicol
Sci 99(1):90–100
18. Fielden MR, Eynon BP, Natsoulis G, Jarnagin K, Banas D, Kolaja KL (2005) A gene expression
signature that predicts the future onset of drug-induced renal tubular toxicity. Toxicol Pathol
33(6):675–683
19. Perez LO, Gonzalez-Jose R, Garcia PP (2016) Prediction of non-genotoxic carcinogenicity
based on genetic profiles of short term exposure assays. Toxicol Res 32(4):289–300
20. Sutherland JJ, Webster YW, Willy JA, Searfoss GH, Goldstein KM, Irizarry AR, Hall DG,
Stevens JL (2018) Toxicogenomic module associations with pathogenesis: a network-based
approach to understanding drug toxicity. Pharmacogenomics J 18(3):377–390
21. Hu W, Sorrentino C, Denison MS, Kolaja K, Fielden MR (2007) Induction of cyp1a1 is a
nonspecific biomarker of aryl hydrocarbon receptor activation: results of large scale screening
of pharmaceuticals and toxicants in vivo and in vitro. Mol Pharmacol 71(6):1475–1486
22. Nault R, Kim S, Zacharewski TR (2013) Comparison of TCDD-elicited genome-wide hepatic gene expression in Sprague-Dawley rats and C57BL/6 mice. Toxicol Appl Pharmacol
267(2):184–191
23. Yu K, Gong B, Lee M, Liu Z, Xu J, Perkins R, Tong W (2014) Discovering functional modules
by topic modeling RNA-Seq based toxicogenomic data. Chem Res Toxicol 27(9):1528–1536
24. AbdulHameed MD, Ippolito DL, Wallqvist A (2016) Predicting rat and human pregnane X
receptor activators using bayesian classification models. Chem Res Toxicol 29(10):1729–1740
25. Tugendreich S, Pearson CI, Sagartz J, Jarnagin K, Kolaja K (2006) NSAID-induced acute phase
response is due to increased intestinal permeability and characterized by early and consistent
alterations in hepatic gene expression. Toxicol Pathol 34(2):168–179
26. Hu G, Agarwal P (2009) Human disease-drug network based on genomic expression profiles.
PLoS ONE 4(8):e6536
27. Iskar M, Zeller G, Blattmann P, Campillos M, Kuhn M, Kaminska KH, Runz H, Gavin AC,
Pepperkok R, van Noort V, Bork P (2013) Characterization of drug-induced transcriptional
modules: towards drug repositioning and functional understanding. Mol Syst Biol 9:662
D. L. Svoboda et al.
9. Natsoulis G, El Ghaoui L, Lanckriet GR, Tolley AM, Leroy F, Dunlea S, Eynon BP, Pearson
CI, Tugendreich S, Jarnagin K (2005) Classification of a large microarray data set: algorithm
comparison and analysis of drug signatures. Genome Res 15(5):724–736
10. Natsoulis G, Pearson CI, Gollub J, Eynon BP, Ferng J, Nair R, Idury R, Lee MD, Fielden
MR, Brennan RJ, Roter AH, Jarnagin K (2008) The liver pharmacological and xenobiotic gene
response repertoire. Mol Syst Biol 4(1):175
11. AbdulHameed MD, Ippolito DL, Stallings JD, Wallqvist A (2016) Mining kidney toxicogenomic data by using gene co-expression modules. BMC Genom 17(1):790
12. Ippolito DL, AbdulHameed MD, Tawa GJ, Baer CE, Permenter MG, McDyre BC, Dennis
WE, Boyle MH, Hobbs CA, Streicker MA, Snowden BS, Lewis JA, Wallqvist A, Stallings JD
(2016) Gene expression patterns associated with histopathology in toxic liver fibrosis. Toxicol
Sci 149(1):67–88
13. AbdulHameed MD, Tawa GJ, Kumar K, Ippolito DL, Lewis JA, Stallings JD, Wallqvist A
(2014) Systems level analysis and identification of pathways and networks associated with
liver fibrosis. PLoS ONE 9(11):e112193
14. Tawa GJ, AbdulHameed MD, Yu X, Kumar K, Ippolito DL, Lewis JA, Stallings JD, Wallqvist A
(2014) Characterization of chemically induced liver injuries using gene co-expression modules.
PLoS ONE 9(9):e107230
15. Gusenleitner D, Auerbach SS, Melia T, Gomez HF, Sherr DH, Monti S (2014) Genomic models
of short-term exposure accurately predict long-term chemical carcinogenicity and identify
putative mechanisms of action. PLoS ONE 9(7):e102579
16. Adler M, Ramm S, Hafner M, Muhlich JL, Gottwald EM, Weber E, Jaklic A, Ajay AK, Svoboda
D, Auerbach S, Kelly EJ, Himmelfarb J, Vaidya VS (2016) A quantitative approach to screen
for nephrotoxic compounds in vitro. J Am Soc Nephrol 27(4):1015–1028
17. Fielden MR, Brennan R, Gollub J (2007) A gene expression biomarker provides early prediction
and mechanistic assessment of hepatic tumor induction by nongenotoxic chemicals. Toxicol
Sci 99(1):90–100
18. Fielden MR, Eynon BP, Natsoulis G, Jarnagin K, Banas D, Kolaja KL (2005) A gene expression
signature that predicts the future onset of drug-induced renal tubular toxicity. Toxicol Pathol
33(6):675–683
19. Perez LO, Gonzalez-Jose R, Garcia PP (2016) Prediction of non-genotoxic carcinogenicity
based on genetic profiles of short term exposure assays. Toxicol Res 32(4):289–300
20. Sutherland JJ, Webster YW, Willy JA, Searfoss GH, Goldstein KM, Irizarry AR, Hall DG,
Stevens JL (2018) Toxicogenomic module associations with pathogenesis: a network-based
approach to understanding drug toxicity. Pharmacogenomics J 18(3):377–390
21. Hu W, Sorrentino C, Denison MS, Kolaja K, Fielden MR (2007) Induction of cyp1a1 is a
nonspecific biomarker of aryl hydrocarbon receptor activation: results of large scale screening
of pharmaceuticals and toxicants in vivo and in vitro. Mol Pharmacol 71(6):1475–1486
22. Nault R, Kim S, Zacharewski TR (2013) Comparison of TCDD-elicited genome-wide hepatic gene expression in Sprague-Dawley rats and C57BL/6 mice. Toxicol Appl Pharmacol
267(2):184–191
23. Yu K, Gong B, Lee M, Liu Z, Xu J, Perkins R, Tong W (2014) Discovering functional modules
by topic modeling RNA-Seq based toxicogenomic data. Chem Res Toxicol 27(9):1528–1536
24. AbdulHameed MD, Ippolito DL, Wallqvist A (2016) Predicting rat and human pregnane X
receptor activators using bayesian classification models. Chem Res Toxicol 29(10):1729–1740
25. Tugendreich S, Pearson CI, Sagartz J, Jarnagin K, Kolaja K (2006) NSAID-induced acute phase
response is due to increased intestinal permeability and characterized by early and consistent
alterations in hepatic gene expression. Toxicol Pathol 34(2):168–179
26. Hu G, Agarwal P (2009) Human disease-drug network based on genomic expression profiles.
PLoS ONE 4(8):e6536
27. Iskar M, Zeller G, Blattmann P, Campillos M, Kuhn M, Kaminska KH, Runz H, Gavin AC,
Pepperkok R, van Noort V, Bork P (2013) Characterization of drug-induced transcriptional
modules: towards drug repositioning and functional understanding. Mol Syst Biol 9:662