Jump to content

Functional element SNPs database

Add links
From Wikipedia, the free encyclopedia
This is an old revision of this page, as edited by Bsheardpinho (talk | contribs) at 01:41, 5 November 2013. The present address (URL) is a permanent link to this revision, which may differ significantly from the current revision.
FESD
Content
DescriptionFunctional Element SNPs Database in human.
OrganismsHomo sapiens
Contact
AuthorsHyo Jin Kang
Primary citationKang & al. (2005)[1]
Access
Websitehttp://combio.kribb.re.kr/ksnp/resd/

The Functional Element SNPs Database (FESD) is a biological database of SNPs in human Molecular biology.[1] The database is a tool designed to organize functional elements into categories in human gene regions and to output their sequences needed for genotyping experiments as well as provide a set of SNPs that lie within each region. The database defines functional elements into ten types: promoter regions, CpG islands,5' untranslated regions (5'-UTRs), translation start sites, splice sites, coding exons, introns, translation stop sites, polyadenylation signals, and 3' UTRs. [2] People may reference this database for haplotype information or obtain a flanking sequence for genotyping.This may help in finding mutations that contribute to common and polygenic diseases. Researchers can manually choose a group of SNPs of special interest for certain functional elements along with their corresponding sequences.[3] The database combines information from sources such as HapMap, UCSC GoldenPath, dbSNP, OMIM, and TRANSFAC. Users can obtain information about tagSNPs and simulate LD blocks for each gene. FESD is still a developing database and is not widely known so was unable to find projects that used the database so I found research using similar databases or databases that are combined in FESD’s information pool.[4]


Research

  • Susceptibility to Myocardial Infarction

The study involved the investigation of ITIH3 (inter alpha trypsin inhibitor heavy chain 3). Researchers used Functional analysis, Linkage disequilibrium mapping,SNP markers, and the HapMap database. FESD Version II may have been used since it has the information from HapMap as well as other databases. The found that the gene was on chromosome 3. In vitro functional analyses showed that this SNP enhanced the transcriptional level of the ITIH3 gene. Furthermore, we found expression of the ITIH3 protein in the vascular smooth muscle cells and macrophages in the human atherosclerotic lesions, suggesting ITIH3 SNP to be a novel genetic risk factor of MI. The gene has been shown to be related to the proinflammatory process of immune response. ITIH3 makes a complex with the locally synthesized hyaluronan (HA) and interacts with inflammatory cells. The ITIH3-HA complex has been reported to be involved in inflammatory diseases, including rheumatoid arthritis and inflammatory bowel diseases. The most statistically-significant SNP did not substitute an amino acid of ITIH3 protein. The researchers hypothesized that this synonymous SNP affected the transcriptional regulation, because several papers reported that some transcriptional factors bound to the exonic coding sequences of some genes and regulated their transcriptional level. There was expression of ITIH3 protein in the atherosclerotic lesion. ITIH3 might play a critical role in the pathogenesis of atherosclerosis and subsequent myocardial infarction. [5]

  • Hepatocellular Carcinoma

These Researchers used snp selecting web tools and again could have used FESD Version II to select their SNPs. They hypothesized that the polymorphisms in circadian genes may be associated with prognosis of hepatocellular carcinoma. The circadian negative feedback regulation genes- CRY1, CRY2, PER1, PER2 and PER3 were identified based on a comprehensive literature review and the potentially functional SNPs were selected through web tools. Finally, a total of twelve potentially functional SNPs in five genes were selected, including CRY1: rs1056560, rs3809236; CRY2: rs6798, rs2292910; PER1: rs2585405, rs3027178; PER2: rs934945, rs2304669; PER3: rs2640908, rs172933, rs2859390, rs228669. When the dominant genetic model was tested, their data showed that only SNP rs2640908 in PER3 gene was significantly associated with overall survival of hepatocellular carcinoma patients. Patients carrying at least one variant allele of rs2640908 had a significantly decreased risk of death when compared with those carrying homozygous wild-type alleles. [6]


  • Rheumatoid Arthritis


References

  1. ^ a b Kang, H. J.; Choi, KO; Kim, BD; Kim, S; Kim, YJ (2004). "FESD: A Functional Element SNPs Database in human". Nucleic Acids Research. 33 (Database issue): D518–22. doi:10.1093/nar/gki082. PMC 540036. PMID 15608252.
  2. ^ MAH, JAMES T. L., and K. S. CHIA. "A Gentle Introduction To Snp Analysis:: Resources And Tools." Journal Of Bioinformatics & Computational Biology 5.5 (2007): 1123-1138. Academic Search Premier. Web. 9 Sept. 2013
  3. ^ Yang, Cheng-Hong; Chuang, Li-Yeh; Cheng, Yu-Huei; Wen, Cheng-Hao; Chang, Hsueh-Wei (2009). "Dynamic Programming for Single Nucleotide Polymorphism ID Identification in Systematic Association Studies". The Kaohsiung Journal of Medical Sciences. 25 (4): 165–76. doi:10.1016/S1607-551X(09)70057-9. PMID 19502133.
  4. ^ Kang, H.J. ( 1,2,3 ), et al. "FESD: A Functional Element Snps Database In Human." Nucleic Acids Research 33.DATABASE ISS. (2005): D518-D522. Scopus®. Web. 4 Nov. 2013
  5. ^ Ebana, Yusuke, et al. "A Functional SNP In ITIH3 Is Associated With Susceptibility To Myocardial Infarction." Journal Of Human Genetics 52.3 (2007): 220-229. Academic Search Premier. Web. 4 Nov. 2013
  6. ^ Zhao, Binyu, et al. "A Functional Polymorphism In PER3 Gene Is Associated With Prognosis In Hepatocellular Carcinoma." Liver International 32.9 (2012): 1451-1459. Academic Search Premier. Web. 4 Nov. 2013.
Retrieved from "https://en.wikipedia.org/w/index.php?title=Functional_element_SNPs_database&oldid=580242401"