The human toxome collaboratorium: A shared environment for multi-omic computational collaboration within a consortium

Frontiers in Pharmacology

Volumn 6, Issue , 2015, Pages

  Fasani, Rick A ^a   Livi, Carolina B ^a   Choudhury, Dipanwita R ^a   Kleensang, Andre ^b   Bouhifd, Mounir ^b   Pendse, Salil N ^c   McMullen, Patrick D ^c   Andersen, Melvin E ^c   Hartung, Thomas ^b,d   Rosenberg, Michael ^a  

^a AGILENT TECHNOLOGIES   (United States)

^b The Johns Hopkins University   (United States)

^c HAMNER INSTITUTES FOR HEALTH SCIENCES   (United States)

^d UNIVERSITY OF KONSTANZ   (Germany)

Author keywords

Big data; Cloud computing; Computational toxicology; Systems toxicology; Virtual machines; Virtualization

Indexed keywords

ANIMAL MODEL; CLOUD COMPUTING; ENDOCRINE SYSTEM; EXPERIMENTAL MODEL; GOVERNMENT; HUMAN; INFORMATION TECHNOLOGY; MACHINE; ORGANIZATION; REPRODUCIBILITY; TOXICITY TESTING; TOXICOLOGY; VISION; WORKFLOW;

EID: 84997170963     PISSN: None     EISSN: 16639812     Source Type: Journal    
DOI: 10.3389/fphar.2015.00322     Document Type: Article

References (30)

1. Adams, J. (2012). Collaborations: the rise of research networks. Nature 490, 335-336. doi: 10.1038/490335a
2. Adams, J. (2013). Collaborations: the fourth age of research. Nature 497, 557-560. doi: 10.1038/497557a
3. Baker, M. (2013). Big biology: the 'omes puzzle. Nature 494, 416-419. doi: 10.1038/494416a
4. Barrett, T., Wilhite, S. E., Ledoux, P., Evangelista, C., Kim, I. F., Tomashevsky, M., et al. (2013). NCBI GEO: archive for functional genomics data sets-update. Nucleic Acids Res. 41, D991-D995. doi: 10.1093/nar/gk s1193
5. Bouhifd, M., Andersen, M. E., Baghdikian, C., Boekelheide, K., Crofton, K. M., Fornace, A. J., et al. (2015). The human toxome project. ALTEX 32, 112-124. doi: 10.14573/altex.1502091
6. Bouhifd, M., Hogberg, H. T., Kleensang, A., Maertens, A., Zhao, L., and Hartung, T. (2014). Mapping the human toxome by systems toxicology. Basic Clin. Pharmacol. Toxicol. 115, 24-31. doi: 10.1111/bcpt.12198
7. Bourdeau, V., Deschênes, J., Laperrière, D., Aid, M., White, J. H., and Mader, S. (2008). Mechanisms of primary and secondary estrogen target gene regulation in breast cancer cells. Nucleic Acids Res. 36, 76-93. doi: 10.1093/nar/gkm945
8. Chang, E. C., Frasor, J., Komm, B., and Katzenellenbogen, B. S. (2006). Impact of estrogen receptor β on gene networks regulated by estrogen receptor α n breast cancer cells. Endocrinology 147, 4831-4842. doi: 10.1210/en.200 6-0563
9. Dahlman-Wright, K., Qiao, Y., Jonsson, P., Gustafsson, J.-Å., Williams, C., and Zhao, C. (2012). Interplay between AP-1 and estrogen receptor α in regulating gene expression and proliferation networks in breast cancer cells. Carcinogenesis 33, 1684-1691. doi: 10.1093/carcin/b gs223
10. Edgar, R., Domrachev, M., and Lash, A. E. (2002). Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30, 207-210. doi: 10.1093/nar/30.1.207
11. Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., et al. (2004). Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, R80. doi: 10.1186/gb-2004-5-10-r80
12. Goecks, J., Nekrutenko, A., Taylor, J., and The Galaxy Team (2010). Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. 11, R86. doi: 10.1186/gb-2010-11-8-r86
13. Gonzalez-Malerva, L., Park, J., Zou, L., Hu, Y., Moradpour, Z., Pearlberg, J., et al. (2011). High-throughput ectopic expression screen for tamoxifen resistance identifies an atypical kinase that blocks autophagy. Proc. Natl. Acad. Sci. U.S.A. 108, 2058-2063. doi: 10.1073/pnas.1018157108
14. Hartung, T., Luechtefeld, T., Maertens, A., and Kleensang, A. (2013). Food for thought::: integrated testing strategies for safety assessments. ALTEX 30, 3-18. doi: 10.14573/altex.2013.1.003
15. Hartung, T., and McBride, M. (2011). Food for thought. on mapping the human toxome. ALTEX 28, 83-93. doi: 10.14573/altex.2011.2.083
16. Hartung, T., van Vliet, E., Jaworska, J., Bonilla, L., Skinner, N., and Thomas, R. (2012). Food for thought. systems toxicology. ALTEX 29, 119-128. doi: 10.14573/altex.2012.2.119
17. Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., et al. (2002). The human genome browser at UCSC. Genome Res. 12, 996-1006. doi: 10.1101/gr.229102
18. Khoury, M. J., and Ioannidis, J. P. A. (2014). Big data meets public health. Science 346, 1054-1055. doi: 10.1126/science.aaa2709
19. Kleensang, A., Maertens, A., Rosenberg, M., Fitzpatrick, S., Lamb, J., Auerbach, S., et al. (2014). t4 workshop report: pathways of toxicity. ALTEX 31, 53-61. doi: 10.14573/altex.1309261
20. Liu, Y., Zhou, J., and White, K. P. (2014). RNA-seq differential expression studies: more sequence or more replication? Bioinformatics 30, 301-304. doi: 10.1093/bioinformatics/btt688
21. Madak-Erdogan, Z., Lupien, M., Stossi, F., Brown, M., and Katzenellenbogen, B. S. (2011). Genomic collaboration of estrogen receptor α and extracellular signal-regulated kinase 2 in regulating gene and proliferation programs. Mol. Cell. Biol. 31, 226-236. doi: 10.1128/MCB.008 21-810
22. Maertens, A., Luechtefeld, T., Kleensang, A., and Hartung, T. (2015). MPTP's Pathway of Toxicity Indicates Central Role of Transcription Factor SP1. Arch. Toxicol. 89, 743-755. doi: 10.1007/s00204-015-1509-6
23. Marx, V. (2013). Biology: the big challenges of big data. Nature 498, 255-260. doi: 10.1038/498255a
24. National Research Council (2007). Toxicity Testing in the 21st Century: A Vision and a Strategy. Washington, DC: The National Academies Press
25. Pendse, S. N., Maertens, A., Rosenberg, M., Roy, D., Fasani, R. A., Vantangoli, M. M., et al. (2016). Information-dependent enrichment analysis reveals timedependent transcriptional regulation of the estrogen pathway of toxicity. bioRxiv doi: 10.1101/038570
26. Perkel, J. M. (2012). Animal-free toxicology: sometimes, in vitro is better. Science 335, 1122-1125. doi: 10.1126/science.335.6072.1122
27. Rae, J. M., Johnson, M. D., Scheys, J. O., Cordero, K. E., Larios, J. M., and Lippman, M. E. (2005). GREB 1 is a critical regulator of hormone dependent breast cancer growth. Breast Cancer Res. Treat. 92, 141-149. doi: 10.1007/s10549-005-1483-4
28. Richardson, T., Stafford-Fraser, Q., Wood, K. R., and Hopper, A. (1998). Virtual network computing. IEEE Internet Comput. 2, 33-38. doi: 10.1109/4236. 656066
29. Soule, H. D., Vazquez, J., Long, A., Albert, S., and Brennan, M. (1973). A human cell line from a pleural effusion derived from a breast carcinoma. J. Natl. Cancer Inst. 51, 1409-1416. doi: 10.1093/jnci/51.5.1409
30. Stephens, M. L., Andersen, M., Becker, R. A., Betts, K., Boekelheide, K., Carney, E., et al. (2013). Evidence-based toxicology for the 21st century: opportunities and challenges. ALTEX 30, 74-103. doi: 10.14573/altex.2013.1.074