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Functional element SNPs database
The Functional Element SNPs Database (FESD) is a biological database of SNPs in Molecular biology.
The database is a tool designed to organize functional elements into categories in human gene regions and to output their sequences needed for genotyping 〔Haja N. Kadarmideen, et al. "Functsnp: An R Package To Link Snps To Functionalknowledge And Dbautomaker: A Suite Of Perlscripts To Build SNP Databases." BMC Bioinformatics 11.(2010): 311-319. Academic Search Premier. Web. 18 Sept. 2013.〕 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. 〔 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〕 People may reference this database for haplotype information or obtain a flanking sequence for genotyping. 〔Chang Hsueh-Wei, et al. "Dynamic Programming For Single Nucleotide Polymorphism ID Identification In Systematic Association Studies." Kaohsiung Journal Of Medical Sciences 25.(n.d.): 165-176. ScienceDirect. Web. 9 Sept. 2013.
〕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. 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.〔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〕
==Uses==
The database is a reference of all known SNPs in functional units that may affect a given phenotype in which some cases may be a disease. You select SNps based on disease, gene, or factor. The database has a link on the HapMap Project website. 〔http://www.khapmap.org〕 The database may very well have been used in one of the following research examples. The Korean HapMap Project website is quoted saying "We have developed a series of software programs for association studies as well as the comparison and analysis of Korean HapMap data with other populations, such as European, Chinese, Japanese, and African populations. The developed soft- ware includes HapMapSNPAnalyzer, SNPflank, HWE Test, FESD, D2GSNP, SNP@Domain, KMSD, KFOD, KFRG, and SNP@WEB."〔Journal Article.ID 5299735. Kim,Young,Uk. Kim,Seung-Ho. Jin,Hoon. Park,Young-Kyu. Ji,Mihyun. Joo,Young. 2008.The Korean HapMap Project Website〕 I am unaware how many species are included; however, there is an alphabetical list of all the genes included in case you know the gene name but not the disease it is associated with or factor it is located in. Some of the genes were from Humans, mice, and some were from D. Melanogaster. Information cannot be submitted to the database publically. The database is updated often and the information is pooled from the sites listed on the page. There is also a user guide tab that shows you what each process should look like.
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