SOP (Search of Omics Pathway): A Web-based Tool for Visualization of KEGG Pathway Diagrams of Omics Data |
Kim, Jun-Sub
(Department of Biochemistry, Hanyang University & GenoCheck Co. Ltd.)
Yeom, Hye-Jung (Department of Biochemistry, Hanyang University & GenoCheck Co. Ltd.) Kim, Seung-Jun (Department of Biochemistry, Hanyang University & GenoCheck Co. Ltd.) Kim, Ji-Hoon (Department of Biochemistry, Hanyang University & GenoCheck Co. Ltd.) Park, Hye-Won (Department of Biochemistry, Hanyang University & GenoCheck Co. Ltd.) Oh, Moon-Ju (Department of Biochemistry, Hanyang University & GenoCheck Co. Ltd.) Hwang, Seung-Yong (Department of Biochemistry, Hanyang University & GenoCheck Co. Ltd.) |
1 | -omics. Wikipedia, the free encyclopedia Available at http://en.wikipedia.org/wiki/-omics. Accessed July 10 (2007) |
2 | Aardema, M. J. & MacGregor, J. T. Toxicology and genetic toxicology in the new era of 'toxicogenomics': impact of '-omics' technologies. Mutat Res 499:13-25 (2002) DOI ScienceOn |
3 | Ulrich, R. & Friend, S. H. Toxicogenomics and drug discovery: will new technologies help us produce better drugs? Nat Rev Drug Discov 1:84-88 (2002) DOI |
4 | Boeckmann, B. et al. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 31:365-370 (2003) DOI ScienceOn |
5 | Waters, M. et al. System's toxicology and the Chemical Effects in Biological Systems (CEBS) knowledge base. EHP Toxicogenomics 111:15-28 (2003) |
6 | Arakawa, K. et al. KEGG-based pathway visualization tool for complex omics data. In Silico Biol 5:419-423 (2005) |
7 | Klukas, C. & Schreiber, F. Dynamic exploration and editing of KEGG pathway diagrams. Bioinformatics 23:344-350 (2007) DOI ScienceOn |
8 | Altermann, E. & Klaenhammer, T. R. PathwayVoyager: pathway mapping using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. BMC Genomics 6:60 (2005) DOI ScienceOn |
9 | Kanehisa, M. et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34:354-357 (2006) DOI ScienceOn |
10 | Arakawa, K. et al. G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining. Bioinformatics 19:305-306 (2003) DOI ScienceOn |
11 | Harris, M. A. et al. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 32: 258-261 (2004) DOI ScienceOn |
12 | Kono, N., Arakawa, K. & Tomita, M. MEGU: pathway mapping web-service based on KEGG and SVG. In Silico Biol 6:621-625 (2006) |
13 | Goto, S. et al. LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res 30:402-404 (2002) DOI ScienceOn |
14 | Lee, W. S. et al. The intelligent data management system for toxicogenomics. J Vet Med Sci 66:1335-1338 (2004) DOI ScienceOn |
15 | Pruitt, K. D., Katz, K. S., Sicotte, H. & Maglott, D. R. Introducing RefSeq and LocusLink: curated human genome resources at the NCBI. Trends Genet 16:44-47 (2000) DOI ScienceOn |
16 | Lee, K. M., Kim, J. H. & Kang, D. Design issues in toxicogenomics using DNA microarray experiment. Toxicol Appl Pharmacol 207:200-208 (2005) DOI ScienceOn |
17 | Kanehisa, M. The KEGG database. Novartis Found Symp 247:91-103, 119-128, 244-252 (2002) DOI |
18 | Orphanides, G. Application of gene expression profile to toxicology. Toxciol Lett 140:145-148 (2003) DOI ScienceOn |
19 | Burchiel, S. W. et al. Analysis of genetic and epigenetic mechanisms of toxicity: potential roles of toxicogenomics and proteomics in toxicology. Toxicol Sci 59:193-195 (2001) DOI ScienceOn |
20 | Benson, D. A. et al. GenBank. Nucleic Acids Res 35: 21-25 (2007) DOI |
21 | Pontius, J. U., Wagner, L. & Schuler, G. D. UniGene: a unified view of the transcriptome. In: The NCBI Handbook. Bethesda (MD): National Center for Biotechnology Information (2003) |
22 | Salomonis, N. et al. GenMAPP 2: new features and resources for pathway analysis. BMC Bioinformatics 24:217 (2007) |
23 | Tong, W. et al. Development of public toxicogenomics software for microarray data management and analysis. Mutat Res 549:241-253 (2004) DOI |
24 | Marchant, G. E. Toxicogenomics and toxic torts. Trends Biotechnol 20:329-323 (2002) DOI ScienceOn |