8 An Overview of National Toxicology Program’s Toxicogenomic …
155
ical assessment of these approaches, which is necessary to vet any new approach to
toxicological assessment.
Future plans for DrugMatrix include regular updating of gene, pathway and ontology annotations, integration of additional pathways from additional sources, and
broadening of the chemical space of the reference genomic data. Integration of available public data sets, expansion of the number of data platforms and species that can
be directly loaded into DrugMatrix for analysis and implementation of APIs to allow
for ease of interaction with other popular genomics analysis tools are also on the
horizon. Recommendations from end users will of significant value. Send any recommendations to Drugmatrix@nih.gov. Where relevant, the data and functionalities
added to DrugMatrix will be implemented in ToxFX.
Acknowledgements The authors would like to acknowledge the large group of former employees
of Iconix Biosciences, in particular, Alan Roter for the original data generation and development
of DrugMatrix and ToxFX. We would also like to acknowledge the ongoing support of the Sciome
LLC and the NTP CEBS database team for support and maintenance of the tools and for help in
disseminating the contents of the database. Finally, the authors would like to thank B. Alex Merrick
for review of the book chapter.
References
1. Fielden MR, Halbert DN (2007) Iconix biosciences, Inc. Pharmacogenomics 8(4):401–405
2. Ganter B, Tugendreich S, Pearson CI, Ayanoglu E, Baumhueter S, Bostian KA, Brady L,
Browne LJ, Calvin JT, Day GJ, Breckenridge N, Dunlea S, Eynon BP, Furness LM, Ferng J,
Fielden MR, Fujimoto SY, Gong L, Hu C, Idury R, Judo MS, Kolaja KL, Lee MD, McSorley
C, Minor JM, Nair RV, Natsoulis G, Nguyen P, Nicholson SM, Pham H, Roter AH, Sun D, Tan
S, Thode S, Tolley AM, Vladimirova A, Yang J, Zhou Z, Jarnagin K (2005) Development of
a large-scale chemogenomics database to improve drug candidate selection and to understand
mechanisms of chemical toxicity and action. J Biotechnol 119(3):219–244
3. Dunnick JK, Pandiri AR, Merrick BA, Kissling GE, Cunny H, Mutlu E, Waidyanatha S, Sills
R, Hong HL, Ton TV, Maynor T, Recio L, Phillips SL, Devito MJ, Brix A (2018) Carcinogenic
activity of pentabrominated diphenyl ether mixture (DE-71) in rats and mice. Toxicol Rep
5:615–624
4. Dunnick JK, Brix A, Cunny H, Vallant M, Shockley KR (2012) Characterization of polybrominated diphenyl ether toxicity in Wistar Han rats and use of liver microarray data for predicting
disease susceptibilities. Toxicol Pathol 40(1):93–106
5. Song R, He Y, Murphy MB, Yeung LW, Yu RM, Lam MH, Lam PK, Hecker M, Giesy JP, Wu
RS, Zhang W, Sheng G, Fu J (2008) Effects of fifteen PBDE metabolites, DE71, DE79 and
TBBPA on steroidogenesis in the H295R cell line. Chemosphere 71(10):1888–1894
6. Sanders JM, Burka LT, Smith CS, Black W, James R, Cunningham ML (2005) Differential
expression of CYP1A, 2B, and 3A genes in the F344 rat following exposure to a polybrominated
diphenyl ether mixture or individual components. Toxicol Sci 88(1):127–133
7. Lin X, Liu YB, Hu H (2017) Metabolic role of fibroblast growth factor 21 in liver, adipose and
nervous system tissues. Biomed Rep 6(5):495–502
8. van der Ven LT, van de Kuil T, Verhoef A, Leonards PE, Slob W, Canton RF, Germer S,
Hamers T, Visser TJ, Litens S, Hakansson H, Fery Y, Schrenk D, van den Berg M, Piersma
AH, Vos JG (2008) A 28-day oral dose toxicity study enhanced to detect endocrine effects of
a purified technical pentabromodiphenyl ether (pentaBDE) mixture in Wistar rats. Toxicology
245(1–2):109–122
155
ical assessment of these approaches, which is necessary to vet any new approach to
toxicological assessment.
Future plans for DrugMatrix include regular updating of gene, pathway and ontology annotations, integration of additional pathways from additional sources, and
broadening of the chemical space of the reference genomic data. Integration of available public data sets, expansion of the number of data platforms and species that can
be directly loaded into DrugMatrix for analysis and implementation of APIs to allow
for ease of interaction with other popular genomics analysis tools are also on the
horizon. Recommendations from end users will of significant value. Send any recommendations to Drugmatrix@nih.gov. Where relevant, the data and functionalities
added to DrugMatrix will be implemented in ToxFX.
Acknowledgements The authors would like to acknowledge the large group of former employees
of Iconix Biosciences, in particular, Alan Roter for the original data generation and development
of DrugMatrix and ToxFX. We would also like to acknowledge the ongoing support of the Sciome
LLC and the NTP CEBS database team for support and maintenance of the tools and for help in
disseminating the contents of the database. Finally, the authors would like to thank B. Alex Merrick
for review of the book chapter.
References
1. Fielden MR, Halbert DN (2007) Iconix biosciences, Inc. Pharmacogenomics 8(4):401–405
2. Ganter B, Tugendreich S, Pearson CI, Ayanoglu E, Baumhueter S, Bostian KA, Brady L,
Browne LJ, Calvin JT, Day GJ, Breckenridge N, Dunlea S, Eynon BP, Furness LM, Ferng J,
Fielden MR, Fujimoto SY, Gong L, Hu C, Idury R, Judo MS, Kolaja KL, Lee MD, McSorley
C, Minor JM, Nair RV, Natsoulis G, Nguyen P, Nicholson SM, Pham H, Roter AH, Sun D, Tan
S, Thode S, Tolley AM, Vladimirova A, Yang J, Zhou Z, Jarnagin K (2005) Development of
a large-scale chemogenomics database to improve drug candidate selection and to understand
mechanisms of chemical toxicity and action. J Biotechnol 119(3):219–244
3. Dunnick JK, Pandiri AR, Merrick BA, Kissling GE, Cunny H, Mutlu E, Waidyanatha S, Sills
R, Hong HL, Ton TV, Maynor T, Recio L, Phillips SL, Devito MJ, Brix A (2018) Carcinogenic
activity of pentabrominated diphenyl ether mixture (DE-71) in rats and mice. Toxicol Rep
5:615–624
4. Dunnick JK, Brix A, Cunny H, Vallant M, Shockley KR (2012) Characterization of polybrominated diphenyl ether toxicity in Wistar Han rats and use of liver microarray data for predicting
disease susceptibilities. Toxicol Pathol 40(1):93–106
5. Song R, He Y, Murphy MB, Yeung LW, Yu RM, Lam MH, Lam PK, Hecker M, Giesy JP, Wu
RS, Zhang W, Sheng G, Fu J (2008) Effects of fifteen PBDE metabolites, DE71, DE79 and
TBBPA on steroidogenesis in the H295R cell line. Chemosphere 71(10):1888–1894
6. Sanders JM, Burka LT, Smith CS, Black W, James R, Cunningham ML (2005) Differential
expression of CYP1A, 2B, and 3A genes in the F344 rat following exposure to a polybrominated
diphenyl ether mixture or individual components. Toxicol Sci 88(1):127–133
7. Lin X, Liu YB, Hu H (2017) Metabolic role of fibroblast growth factor 21 in liver, adipose and
nervous system tissues. Biomed Rep 6(5):495–502
8. van der Ven LT, van de Kuil T, Verhoef A, Leonards PE, Slob W, Canton RF, Germer S,
Hamers T, Visser TJ, Litens S, Hakansson H, Fery Y, Schrenk D, van den Berg M, Piersma
AH, Vos JG (2008) A 28-day oral dose toxicity study enhanced to detect endocrine effects of
a purified technical pentabromodiphenyl ether (pentaBDE) mixture in Wistar rats. Toxicology
245(1–2):109–122