DOI QR코드

DOI QR Code

DMBase: An Integrated Genetic Information Resource for Diabetes Mellitus

  • Received : 2011.03.31
  • Accepted : 2011.04.06
  • Published : 2011.06.30

Abstract

Diabetes Mellitus (DM), often simply referred to as diabetes, has developed into a major health concern affecting more than 200 million people worldwide with approximately 4 million deaths per year attributed to the presence of the disease. Diabetes mellitus is categorized as Type 1 and Type 2, where Type 1 diabetes represents a lack of insulin production, and Type 2 diabetes is characterized by a relative lack of insulin receptor (i.e., decreased sensitivity to the effect of insulin) and cased by a complex interplay between genetic factors and environmental factors. Up to date, various studies on the pathology and mechanism in terms of genetic experiments have been conducted and approximately hundreds of genes were reported as diabetes mellitus associated genes. At this point, to support studies on the cause and mechanism of diabetes mellitus, an efficient database system to provide genetic variants related to diabetes mellitus is needed. DMBase is an integrated web-based genetic information resource for diabetes mellitus designed to service genomic variants, genes, and secondary information derived for diabetes mellitus genetics researchers. The current version of DMBase documents 754 genes with 3056 genetic variants and 66 pathways. It provides many effective search interfaces for retrieving diabetes mellitus and genetic information. A web interface for the DMBase is freely available at http://sysbio.kribb.re.kr/dmBase.

References

  1. Grant, S.F., and Hakonarson, H. (2009). Genome-wide association studies in type 1 diabetes. Curr Diab Rep 9, 157-163. https://doi.org/10.1007/s11892-009-0026-5
  2. Hulbert, E.M., Smink, L.J., Adlem, E.C., Allen, J.E., Burdick, D.B., Burren, O.S., Cassen, V.M., Cavnor, C.C., Dolman, G.E., Flamez, D., et al. (2007). T1DBase: integration and presentation of complex data for type 1 diabetes research. Nucleic Acids Res 35, D742-746. https://doi.org/10.1093/nar/gkl933
  3. McCarthy, M.I., and Zeggini, E. (2009). Genome-wide association studies in type 2 diabetes. Curr Diab Rep 9, 164-171. https://doi.org/10.1007/s11892-009-0027-4
  4. Zeggini, E., and McCarthy, M.I. (2007). Identifying susceptibility variants for type 2 diabetes. Methods Mol Biol 376, 235-250. https://doi.org/10.1007/978-1-59745-389-9_16
  5. Agrawal, S., Dimitrova, N., Nathan, P., Udayakumar, K., Lakshmi, S.S., Sriram, S., Manjusha, N., and Sengupta, U. (2008). T2D-Db: an integrated platform to study the molecular basis of Type 2 diabetes. BMC Genomics 9, 320. https://doi.org/10.1186/1471-2164-9-320
  6. Mazzarelli, J.M., Brestelli, J., Gorski, R.K., Liu, J., Manduchi, E., Pinney, D.F., Schug, J., White, P., Kaestner, K.H., and Stoeckert, C.J., Jr. (2007). EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes. Nucleic Acids Res 35, D751-755. https://doi.org/10.1093/nar/gkl748
  7. Perry, J.R., McCarthy, M.I., Hattersley, A.T., Zeggini, E., Weedon, M.N., and Frayling, T.M. (2009). Interrogating type 2 diabetes genome-wide association data using a biological pathway-based approach. Diabetes 58, 1463-1467 https://doi.org/10.2337/db08-1378
  8. Amberger, J., Bocchini, C.A., Scott, A.F., and Hamosh, A. (2009). McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res 37, D793-796. https://doi.org/10.1093/nar/gkn665
  9. UniProt consortium. (2009). The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res 38, D142-148.
  10. Sherry, S.T., Ward, M.H., Kholodov, M., Baker, J., Phan, L., Smigielski, E.M., and Sirotkin, K. (2001). dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29, 308-311. https://doi.org/10.1093/nar/29.1.308
  11. Rhead, B., Karolchik, D., Kuhn, R.M., Hinrichs, A.S., Zweig, A.S., Fujita, P.A., Diekhans, M., Smith, K.E., Rosenbloom, K.R., Raney, B.J., et al. (2010). The UCSC Genome Browser database: update 2010. Nucleic Acids Res 38, D613-619. https://doi.org/10.1093/nar/gkp939
  12. Povey, S., Lovering, R., Bruford, E., Wright, M., Lush, M., and Wain, H. (2001). The HUGO Gene Nomenclature Committee (HGNC). Hum Genet 109, 678-680. https://doi.org/10.1007/s00439-001-0615-0
  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., et al. (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102, 15545-15550. https://doi.org/10.1073/pnas.0506580102
  14. HUGO Gene Nomenclature Committee (HGNC). http://www. genenames.org.
  15. The Molecular Signatures Database (MSigDB). http://www.broadinstitute.org/gsea/msigdb.
  16. UCSC Genome Bioinformatics. http://genome.ucsc.edu.