FESD II: A Revised Functional Element SNP Database of Human Ethnicities

  • Kim, Hyun-Ju (Korea Research Institute of Bioscience and Biotechnology) ;
  • Kim, Il-Hyun (Korea Research Institute of Bioscience and Biotechnology) ;
  • Shin, Ki-Hoon (Korea Research Institute of Bioscience and Biotechnology) ;
  • Park, Young-Kyu (Korea Research Institute of Bioscience and Biotechnology) ;
  • Kang, Hyo-Jin (Department of Bio and Brain, KAIST) ;
  • Kim, Young-Joo (Korea Research Institute of Bioscience and Biotechnology)
  • Published : 2007.12.31

Abstract

The Functional Element SNPs Database (FESD) categorizes functional elements in human genic regions and provides a set of single nucleotide polymorphisms (SNPs) located within each area. Users may select a set of SNPs in specific functional elements with haplotype information and obtain flanking sequences for genotyping. Our previous version of FESD has been improved in several ways. We regenerated all the data in FESD II from recently updated source data such as HapMap, UCSC GoldenPath, dbSNP, OMIM, and $TRANSFAC^{(R)}$. Users can obtain information about tagSNPs and simulate LD blocks for each gene from four ethnicities in the HapMap project on the fly. FESD II employs a Java/JSP web interface for better platform portability and higher speed than PHP in the previous version. As a result, FESD II provides its users with more powerful information about functional element SNPs of human ethnicities.

Keywords

SNP;tagSNP;haplotype;functional elements;LD block;hapMap

References

  1. Karolchik, D., Hinrichs, A.S., et al. (2004). The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 32(Database issue). D493-D496 https://doi.org/10.1093/nar/gkh103
  2. Marchini, J., Howie, B., et al. (2007). A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet. 39(7). 906-913 https://doi.org/10.1038/ng2088
  3. Nothnagel, M., Furst, R., et al. (2002). Entropy as a measure for linkage disequilibrium over multilocus haplotype blocks. Hum Hered. 54(4). 186-198 https://doi.org/10.1159/000070664
  4. Ring, H.Z., and Kroetz, D.L. (2002). Candidate gene approach for pharmacogenetic studies. Pharmacogenomics 3(1). 47-56 https://doi.org/10.1517/14622416.3.1.47
  5. Wise, C.A., Paris, M., et al. (2003). A standard protocol for single nucleotide primer extension in the human genome using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun Mass Spectrom. 17(11). 1195-1202 https://doi.org/10.1002/rcm.1038
  6. Benson, D.A., Karsch-Mizrachi, I., et al. (2004). GenBank: update. Nucleic Acids Res 32(Database issue). D23-D26 https://doi.org/10.1093/nar/gkh045
  7. Zhang, K., Qin, Z.S., et al. (2004). Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies. Genome Res. 14(5). 908-916 https://doi.org/10.1101/gr.1837404
  8. Stranger, B.E., Forrest, M.S., et al. (2007). Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315(5813). 848-853 https://doi.org/10.1126/science.1136678
  9. Kang, H.J., Choi, K.O., et al. (2005). FESD: a Functional Element SNPs Database in human. Nucleic Acids Res. 33(Database issue). D518- D522 https://doi.org/10.1093/nar/gki082
  10. Barrett, J.C., Fry, B., et al. (2005). Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21(2). 263-265 https://doi.org/10.1093/bioinformatics/bth457
  11. de Bakker, P.I., Yelensky, R., et al. (2005). Efficiency and power in genetic association studies. Nat Genet. 37(11). 1217-1223 https://doi.org/10.1038/ng1669
  12. Jung, H.Y., Park, J.S., et al. (2004). HapAnalyzer: Minimum Haplotype Analysis System for Association Studies. Genomics &Informatics 2(2). 107-109
  13. Karolchik, D., Baertsch, R., et al. (2003). The UCSC Genome Browser Database. Nucleic Acids Res. 31(1). 51-54 https://doi.org/10.1093/nar/gkg129
  14. Maglott, D., Ostell, J., et al. (2005). Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res. 33(Database issue). D54-D58 https://doi.org/10.1093/nar/gni052
  15. Kel, A.E., Gossling, E., et al. (2003). MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res. 31(13). 3576-3579 https://doi.org/10.1093/nar/gkg585
  16. Sherry, S.T., Ward, M.H., et al. (2001). dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 29(1). 308-311 https://doi.org/10.1093/nar/29.1.308
  17. Wheeler, D.L., Barrett, T., et al. (2007). Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 35(Database issue). D5-D12 https://doi.org/10.1093/nar/gkl1031
  18. Kent, W.J., Sugnet, C.W., et al. (2002). The human genome browser at UCSC. Genome Res. 12(6). 996-1006 https://doi.org/10.1101/gr.229102