Skip to main content
NCBI home page
Environmental Health Perspectives logoLink to Environmental Health Perspectives
. 2003 May;111(6):793–795. doi: 10.1289/ehp.6028

The Comparative Toxicogenomics Database (CTD).

Carolyn J Mattingly 1, Glenn T Colby 1, John N Forrest 1, James L Boyer 1
PMCID: PMC1241500  PMID: 12760826

Abstract

The Mount Desert Island Biological Laboratory in Salsbury Cove, Maine, USA, is developing the Comparative Toxicogenomics Database (CTD), a community-supported genomic resource devoted to genes and proteins of human toxicologic significance. CTD will be the first publicly available database to a) provide annotated associations among genes, proteins, references, and toxic agents, with a focus on annotating data from aquatic and mammalian organisms; b) include nucleotide and protein sequences from diverse species; c) offer a range of analysis tools for customized comparative studies; and d) provide information to investigators on available molecular reagents. This combination of features will facilitate cross-species comparisons of toxicologically significant genes and proteins. These comparisons will promote understanding of molecular evolution, the significance of conserved sequences, the genetic basis of variable sensitivity to environmental agents, and the complex interactions between the environment and human health. CTD is currently under development, and the planned scope and functions of the database are described herein. The intent of this report is to invite community participation in the development of CTD to ensure that it will be a valuable resource for environmental health, molecular biology, and toxicology research.

Full Text

The Full Text of this article is available as a PDF (113.8 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Aller S. G., Lombardo I. D., Bhanot S., Forrest J. N., Jr Cloning, characterization, and functional expression of a CNP receptor regulating CFTR in the shark rectal gland. Am J Physiol. 1999 Feb;276(2 Pt 1):C442–C449. doi: 10.1152/ajpcell.1999.276.2.C442. [DOI] [PubMed] [Google Scholar]
  2. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  3. Aparicio Samuel, Chapman Jarrod, Stupka Elia, Putnam Nik, Chia Jer-Ming, Dehal Paramvir, Christoffels Alan, Rash Sam, Hoon Shawn, Smit Arian. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science. 2002 Jul 25;297(5585):1301–1310. doi: 10.1126/science.1072104. [DOI] [PubMed] [Google Scholar]
  4. Ballatori Nazzareno, Villalobos Alice R. Defining the molecular and cellular basis of toxicity using comparative models. Toxicol Appl Pharmacol. 2002 Sep 15;183(3):207–220. doi: 10.1006/taap.2002.9488. [DOI] [PubMed] [Google Scholar]
  5. Baxevanis Andreas D. The Molecular Biology Database Collection: 2002 update. Nucleic Acids Res. 2002 Jan 1;30(1):1–12. doi: 10.1093/nar/30.1.1. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Benson Dennis A., Karsch-Mizrachi Ilene, Lipman David J., Ostell James, Rapp Barbara A., Wheeler David L. GenBank. Nucleic Acids Res. 2002 Jan 1;30(1):17–20. doi: 10.1093/nar/30.1.17. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Blake Judith A., Richardson Joel E., Bult Carol J., Kadin Jim A., Eppig Janan T., Mouse Genome Database Group The Mouse Genome Database (MGD): the model organism database for the laboratory mouse. Nucleic Acids Res. 2002 Jan 1;30(1):113–115. doi: 10.1093/nar/30.1.113. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Cai S. Y., Wang L., Ballatori N., Boyer J. L. Bile salt export pump is highly conserved during vertebrate evolution and its expression is inhibited by PFIC type II mutations. Am J Physiol Gastrointest Liver Physiol. 2001 Aug;281(2):G316–G322. doi: 10.1152/ajpgi.2001.281.2.G316. [DOI] [PubMed] [Google Scholar]
  9. Cai Shi-Ying, Wang Wei, Soroka Carol J., Ballatori Nazzareno, Boyer James L. An evolutionarily ancient Oatp: insights into conserved functional domains of these proteins. Am J Physiol Gastrointest Liver Physiol. 2002 Apr;282(4):G702–G710. doi: 10.1152/ajpgi.00458.2001. [DOI] [PubMed] [Google Scholar]
  10. Dooley K., Zon L. I. Zebrafish: a model system for the study of human disease. Curr Opin Genet Dev. 2000 Jun;10(3):252–256. doi: 10.1016/s0959-437x(00)00074-5. [DOI] [PubMed] [Google Scholar]
  11. Gamba G., Saltzberg S. N., Lombardi M., Miyanoshita A., Lytton J., Hediger M. A., Brenner B. M., Hebert S. C. Primary structure and functional expression of a cDNA encoding the thiazide-sensitive, electroneutral sodium-chloride cotransporter. Proc Natl Acad Sci U S A. 1993 Apr 1;90(7):2749–2753. doi: 10.1073/pnas.90.7.2749. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Hahn Mark E. Aryl hydrocarbon receptors: diversity and evolution. Chem Biol Interact. 2002 Sep 20;141(1-2):131–160. doi: 10.1016/s0009-2797(02)00070-4. [DOI] [PubMed] [Google Scholar]
  13. Koonin E. V., Aravind L., Kondrashov A. S. The impact of comparative genomics on our understanding of evolution. Cell. 2000 Jun 9;101(6):573–576. doi: 10.1016/s0092-8674(00)80867-3. [DOI] [PubMed] [Google Scholar]
  14. Lipscomb C. E. Medical Subject Headings (MeSH). Bull Med Libr Assoc. 2000 Jul;88(3):265–266. [PMC free article] [PubMed] [Google Scholar]
  15. O'Donovan Claire, Martin Maria Jesus, Gattiker Alexandre, Gasteiger Elisabeth, Bairoch Amos, Apweiler Rolf. High-quality protein knowledge resource: SWISS-PROT and TrEMBL. Brief Bioinform. 2002 Sep;3(3):275–284. doi: 10.1093/bib/3.3.275. [DOI] [PubMed] [Google Scholar]
  16. Poland A., Knutson J. C. 2,3,7,8-tetrachlorodibenzo-p-dioxin and related halogenated aromatic hydrocarbons: examination of the mechanism of toxicity. Annu Rev Pharmacol Toxicol. 1982;22:517–554. doi: 10.1146/annurev.pa.22.040182.002505. [DOI] [PubMed] [Google Scholar]
  17. Pruitt K. D., Maglott D. R. RefSeq and LocusLink: NCBI gene-centered resources. Nucleic Acids Res. 2001 Jan 1;29(1):137–140. doi: 10.1093/nar/29.1.137. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Russom Christine L. Mining environmental toxicology information: web resources. Toxicology. 2002 Apr 25;173(1-2):75–88. doi: 10.1016/s0300-483x(02)00023-9. [DOI] [PubMed] [Google Scholar]
  19. Schmidt J. V., Bradfield C. A. Ah receptor signaling pathways. Annu Rev Cell Dev Biol. 1996;12:55–89. doi: 10.1146/annurev.cellbio.12.1.55. [DOI] [PubMed] [Google Scholar]
  20. Sprague J., Doerry E., Douglas S., Westerfield M. The Zebrafish Information Network (ZFIN): a resource for genetic, genomic and developmental research. Nucleic Acids Res. 2001 Jan 1;29(1):87–90. doi: 10.1093/nar/29.1.87. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Thomas Russell S., Penn Sharron G., Holden Kevin, Bradfield Christopher A., Rank David R. Sequence variation and phylogenetic history of the mouse Ahr gene. Pharmacogenetics. 2002 Mar;12(2):151–163. doi: 10.1097/00008571-200203000-00009. [DOI] [PubMed] [Google Scholar]
  22. Thompson J. D., Higgins D. G., Gibson T. J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994 Nov 11;22(22):4673–4680. doi: 10.1093/nar/22.22.4673. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Wexler P. TOXNET: an evolving web resource for toxicology and environmental health information. Toxicology. 2001 Jan 12;157(1-2):3–10. doi: 10.1016/s0300-483x(00)00337-1. [DOI] [PubMed] [Google Scholar]
  24. Whelan S., Liò P., Goldman N. Molecular phylogenetics: state-of-the-art methods for looking into the past. Trends Genet. 2001 May;17(5):262–272. doi: 10.1016/s0168-9525(01)02272-7. [DOI] [PubMed] [Google Scholar]
  25. Wittbrodt Joachim, Shima Akihiro, Schartl Manfred. Medaka--a model organism from the far East. Nat Rev Genet. 2002 Jan;3(1):53–64. doi: 10.1038/nrg704. [DOI] [PubMed] [Google Scholar]
  26. Xu J. C., Lytle C., Zhu T. T., Payne J. A., Benz E., Jr, Forbush B., 3rd Molecular cloning and functional expression of the bumetanide-sensitive Na-K-Cl cotransporter. Proc Natl Acad Sci U S A. 1994 Mar 15;91(6):2201–2205. doi: 10.1073/pnas.91.6.2201. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Young Robert R. Genetic toxicology: web resources. Toxicology. 2002 Apr 25;173(1-2):103–121. doi: 10.1016/s0300-483x(02)00026-4. [DOI] [PubMed] [Google Scholar]

Articles from Environmental Health Perspectives are provided here courtesy of National Institute of Environmental Health Sciences

RESOURCES