XPERNATO-TOX: an Integrated Toxicogenomics Knowledgebase |
Woo Jung-Hoon
(Seoul National University Biomedical Informatics (SNUBI))
Kim Hyeoun-Eui (Graduate Program in Health Informatics, University of Minnesota, Minneapolis) Kong Gu (Department of Pathology, College of Medicine and Molecular Biomarker Research Center, Hanyang University) Kim Ju-Han (Seoul National University Biomedical Informatics (SNUBI) and Human Genome Research Institute, Seoul National University College of Medicine) |
1 | Mattes,W.B., Pettit, S.D., Sansone,S.A., Bushel, P.R.,and Waters, M.D. (2004). Database development in toxicog enomics: issues and efforts. Environ. Health Perspect. 112, 495-505 DOI ScienceOn |
2 | Bolstad, B.M., Irizarry, R.A, Astrand, M., and Speed, T.P. (2003). A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185-193 DOI ScienceOn |
3 | Tusher, V.G., libshirani, R., and Chu, G. (2001). Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA 98, 5116-5121 |
4 | Saidi, S.A., Holland, C.M., Kreil, D.P., MacKay, D.J., Charnock-Jones, D.S., Print, C.G., and Smith, S.K. (2004). Independent component analysis of microarray data in the study of endometrial cancer. Oncogene 23, 6677-6683 DOI ScienceOn |
5 | Tibshirani, R., Hastie, T., Narasimhan, B., and Chu, G. (2002). Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc. Natl. Acad. Sci. USA 99, 6567-6572 |
6 | Hamosh, A, Scott, A.F., Amberger, J.S., Bocchini, C.A, and McKusick,V.A. (2001). Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 30, 52-55 |
7 | Tong, W., Cao, X., Harris, S., Sun, H., Fang, H., Fuscoe, J., Harris, A., Hong, H., Xie, Q., Perkins, R., Shi, L., and Casciano, D. (2003). ArrayTrack-supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research. Environ Health Perspect.111, 1819-1826 DOI ScienceOn |
8 | Lee, H.W., Park, Y.R., Sim, J.H., Park, R.W., Kim, W.H., and Kim, J.H. The Tissue Microarray Object Model: a data model for storage, analysis and exchange of tissue microarray experimental data, Archives of Pathology and Laboratory Medicine, accepted |
9 | Laura, S., Lee, E.B., and Eric B.W. (2004).Toxicogenomics in PredictiveToxicologyin DrugDevelopment. Chemistry & Biology 11,161-171 DOI |
10 | Michael, D.W., Kenneth, O., and Raymond, W.T. (2003). Toxicogenomic approach for assessing toxicant-related disease. Mutation Research 544, 415-424 DOI ScienceOn |
11 | Benson, D.A., Boguski, M., Lipman, D.J., and Ostell, J. (1994). GenBank. Nucleic Acids Res. 22, 3441-3444 DOI |
12 | Baldi, P. and Long, A.D. (2001). A Bayesian Framework for the Analysis of Microarray Expression Data: Regularized t-Test and Statistical Inferences of Gene Changes. Bioinformatics 17, 509-519 DOI ScienceOn |
13 | Subramanian, A., Tamayo, P., Mootha, V.K., Mukherjee, S., Ebert, B.L., Gillette, M.A., Paulovich, A., Pomeroy, S.L., Golub, T.R., Lander, E.S., and Mesirov, J.P. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-Wide expression profiles. Proc. Natl. Acad. Sci. USA 102,15545-15550 |
14 | Aardema, M.J.and MacGregor, J.T. (2002).Toxicologyand genetic toxicology in the new era of 'toxicogenomics': impact of '-omics' technologies. Mutat. Res. 499,13-25 DOI ScienceOn |
15 | Mattingly, C.J., Colby, G.T., Rosenstein, M.C., Forrest, J.N.Jr, Boyer, J.L. (2003). The Comparative Toxicogeno mics Database (CTD). Environmental Health Perspectives. 111, 6 |
16 | Brown, M.P., Grundy, W.N., Lin, D., Cristianini, N., Sugnet, C.W., Furey, T.S., Ares, M. and Jr Haussler, D. (2000). Knowledge-based analysis of microarraygene expression data by using support vector machines. Proc. Natl. Acad. Sci. USA 97, 262-267 |
17 | Yang, Y.H., Xiao, Y., and Segal, M.R. (2005). Identifying differentially expressed genes from microarray experiments via statistic synthesis. Bioinformatics 21, 1084-1093 DOI ScienceOn |
18 | Huber, W., von Heydebreck, A., Sultmann, H., Poustka, A., and Vingron, M. (2002). Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 1, 1-9 |
19 | Michael, D.W. and Jennifer, M.F. (2004). TOXICOGE NOMICS AND SYSTEMS TOXICOLOGY: AIMS AND PROSPECTS, Nature Genet. 5, 936-948 DOI ScienceOn |
20 | Hamadeh, H.K., Amin, R.P., Paules, R.S.,and Afshari,C.A. (2002). An overview of toxicogenomics. Curr. Issues Mol. BioI. 4, 45-56 |