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Korean Society for Biochemistry and Molecular Biology (생화학분자생물학회)
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GEDA: New Knowledge Base of Gene Expression in Drug Addiction

  • Suh, Young-Ju (The Research Institute of Natural Sciences, Sookmyung Women's University) ;
  • Yang, Moon-Hee (Research Center for Women's Diseases, Department of Biological Sciences, Sookmyung Women's University) ;
  • Yoon, Suk-Joon (Research Center for Women's Diseases, Department of Biological Sciences, Sookmyung Women's University) ;
  • Park, Jong-Hoon (Research Center for Women's Diseases, Department of Biological Sciences, Sookmyung Women's University)
  • Received : 2006.04.01
  • Accepted : 2006.04.30
  • Published : 2006.07.31
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Abstract

Abuse of drugs can elicit compulsive drug seeking behaviors upon repeated administration, and ultimately leads to the phenomenon of addiction. We developed a procedure for the standardization of microarray gene expression data of rat brain in drug addiction and stored them in a single integrated database system, focusing on more effective data processing and interpretation. Another characteristic of the present database is that it has a systematic flexibility for statistical analysis and linking with other databases. Basically, we adopt an intelligent SQL querying system, as the foundation of our DB, in order to set up an interactive module which can automatically read the raw gene expression data in the standardized format. We maximize the usability of this DB, helping users study significant gene expression and identify biological function of the genes through integrated up-to-date gene information such as GO annotation and metabolic pathway. For collecting the latest information of selected gene from the database, we also set up the local BLAST search engine and non-redundant sequence database updated by NCBI server on a daily basis. We find that the present database is a useful query interface and data-mining tool, specifically for finding out the genes related to drug addiction. We apply this system to the identification and characterization of methamphetamine-induced genes' behavior in rat brain.

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References

  1. Ahmed, S. H., Lutjens, R., van der Stap, L. D., Lekic, D., Romano-Spica, V., Morales, M., Koob, G. F., Repunte-Canonigo, V. and Sanna, P. P. (2005) Gene expression evidence for remodeling of lateral hypothalamic circuitry in cocaine addiction. Proc. Natl. Acad. Sci. USA 102, 11533-11538 https://doi.org/10.1073/pnas.0504438102
  2. Alberts, R., Fu, J., Swertz, M. A., Lubbers, L. A., Albers, C. J. and Jansen, R. C. (2005) Combining microarrays and genetic analysis. Brief Bioinform. 6, 135-145 https://doi.org/10.1093/bib/6.2.135
  3. Albertson, D. N., Pruetz, B., Schmidt, C. J., Kuhn, D. M., Kapatos, G. and Bannon, M. J. (2004) Gene expression profile of the nucleus accumbens of human cocaine abusers: evidence for dysregulation of myelin. J. Neurochem. 88, 1211-1219 https://doi.org/10.1046/j.1471-4159.2003.02247.x
  4. Arlinde, C., Sommer, W., Bjork, K., Reimers, M., Hyytia, P., Kiianmaa, K. and Heilig, M. (2004) A cluster of differentially expressed signal transduction genes identified by microarray analysis in a rat genetic model of alcoholism. Pharmacogenomics J. 4, 208-218 https://doi.org/10.1038/sj.tpj.6500243
  5. Bahi, A. and Dreyer, J. L. (2005) Cocaine-induced expression changes of axon guidance molecules in the adult rat brain. Mol. Cell. Neurosci. 28, 275-291 https://doi.org/10.1016/j.mcn.2004.09.011
  6. Burgoon, L. D., Boutros, P. C., Dere, E. and Zacharewski, T. R. (2006) dbZach: A MIAME-compliant toxicogenomic supportive relational database. Toxicol. Sci. 90, 558-568 https://doi.org/10.1093/toxsci/kfj097
  7. Everitt, B. J. and Robbins, T. W. (2005) Neural systems of reinforcement for drug addiction: from actions to habits to compulsion. Nat. Neurosci. 8, 1481-1489 https://doi.org/10.1038/nn1579
  8. Fei, Z., Tang, X., Alba, R. and Giovannoni, J. (2006) Tomato Expression Database (TED): a suite of data presentation and analysis tools. Nucl. Acids Res. 34, 766-770 https://doi.org/10.1093/nar/gkj110
  9. Funada, M., Zhou, X., Satoh, M. and Wada, K. (2004) Profiling of methamphetamine-induced modifications of gene expression patterns in the mouse brain. Ann. N. Y. Acad. Sci. 1025, 76-83 https://doi.org/10.1196/annals.1316.010
  10. Hawes, J. and Piccotto, M. R. (2004) Characterizatoin of GalR1, GalR2, and GalR3 immunoreactivity in catecholaminergic nuclei of the mouse brain. J. Comp. Neurol. 479, 410-423 https://doi.org/10.1002/cne.20329
  11. Ishigami, A., Tokunaga, I., Gotohda, T. and Kubo, S. (2003) Immunohistochemical study of myoglobin and oxidative injury related markers in the kidney of methamphetamine abusers. Leg. Med. (Tokyo) 5, 42-48 https://doi.org/10.1016/S1344-6223(03)00005-1
  12. Iwamoto, K., Bundo, M., Yamamoto, M., Ozawa, H., Saito, T. and Kato, T. (2004) Decreased expression of NEFH and PCP4/PEP19 in the prefrontal cortex of alcoholics. Neurosci. Res. 49, 379-385 https://doi.org/10.1016/j.neures.2004.04.002
  13. Klag, S., O'Callaghan, F. and Creed, P. (2005) The use of legal coercion in the treatment of substance abusers: an overview and critical analysis of thirty years of research. Subst. Use Misuse. 40, 1777-1795 https://doi.org/10.1080/10826080500260891
  14. Leibowitz, S. F., Avena, N. M., Chang, G.. Q., Karatayev, O., Chau, D. T. and Hoebel, B. G.. (2003) Ethanol intake increases galanin mRNA in the hypothalamus and withdrawal decreases it. Physiol. Behav. 79, 103-111 https://doi.org/10.1016/S0031-9384(03)00110-0
  15. McClung, C. A. and Nestler, E. J. (2003) Regulation of gene expression and cocaine reward by CREB and DeltaFosB. Nat. Neurosci. 6, 1208-1215 https://doi.org/10.1038/nn1143
  16. Miyamoto, Y., Yamada, K., Nagai, T., Mori, H., Mishina, M., Furukawa, H., Noda, Y. and Nabeshima, T. (2004) Behavioural adaptations to addictive drugs in mice lacking the NMDA receptor epsilon1 subunit. Eur. J. Neurosci. 19, 151-158 https://doi.org/10.1111/j.1460-9568.2004.03086.x
  17. Nestler, E. J. (2001) Molecular basis of long-term plasticity underlying addiction. Nat. Rev. Neurosci. 2, 119-128 https://doi.org/10.1038/35053570
  18. Noailles, P. A., Becker, K. G., Wood, W. H. 3rd, Teichberg, D. and Cadet, J. L. (2003) Methamphetamine-induced gene expression profiles in the striatum of male rat pups exposed to the drug in utero. Brain Res. Dev. Brain Res. 147, 153-162 https://doi.org/10.1016/j.devbrainres.2003.11.003
  19. Picciotto, M. R., Hawes, J. J., Brunzell, D. H. and Zachariou, V. (2005) Galanin can attenuate opiate reinforcement and withdrawal. Neuropeptides 39, 313-315 https://doi.org/10.1016/j.npep.2004.12.001
  20. Rouse, R. and Hardiman, G. (2003) Microarray technology--intellectual property retrospective. Pharmacogenomics 4, 623-632 https://doi.org/10.1517/phgs.4.5.623.23792
  21. Sommer, W., Arlinde, C. and Heilig, M. (2005) The search for candidate genes of alcoholism: evidence from expression profiling studies. Addict. Biol. 10, 71-79 https://doi.org/10.1080/13556210412331327821
  22. Thomas, D. M., Francescutti-Verbeem, D. M., Liu, X. and Kuhn, D. M. (2004) Identification of differentially regulated transcripts in mouse striatum following methamphetamine treatment--an oligonucleotide microarray approach. J. Neurochem. 88, 380-393 https://doi.org/10.1046/j.1471-4159.2003.02182.x
  23. Yamada, K., Nagai, T. and Nabeshima, T. (2005) Drug dependence, synaptic plasticity, and tissue plasminogen activator. J. Pharmacol. Sci. 97, 157-161 https://doi.org/10.1254/jphs.CP0040014
  24. Yamamoto, H., Imai, K., Takamatsu, Y., Kamegaya, E., Kishida, M., Hagino, Y., Hara, Y., Shimada, K., Yamamoto, T., Sora, I., Koga, H. and Ikeda, K. (2005) Methamphetamine modulation of gene expression in the brain: analysis using customized cDNA microarray system with the mouse homologues of KIAA genes. Brain Res. Mol. Brain Res. 137, 40-46 https://doi.org/10.1016/j.molbrainres.2005.02.028
  25. Zhao, R. J., Woo, R. S., Jeong, M. S., Shin, B. S., Kim, D. G. and Kim, K. W. (2003) Orphanin FQ/nociceptin blocks methamphetamine place preference in rats. Neuroreport. 14, 2383-2385 https://doi.org/10.1097/00001756-200312190-00019