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SNPTrack stores and organizes study data and provides access to functional information about the SNPs in a study, including information about the genes and
proteins containing a SNP and Gene Ontology information and pathway information available for those genes and proteins. The client application integrates the popular analysis tools PLINK and Haploview with the storage and interpretation capabilities developed for ArrayTrack™.
Like ArrayTrack™, SNPTrack consists of three major components: StudyDB, TOOL, and LIB.
- StudyDB hosts and manages genetic data and related study data. It supports text-based importing and exporting of study data including SNP panel annotation, genotypes, and phenotypes. It also enables the user to manage SNP lists and make comparisons across analyses using Venn diagrams. Different types of data are organized and presented in a tree-structured view of three node types: study owner or group, study, and study data.
- The TOOL component contains external tools for genetic data analysis. Data are formatted and exported to the client computer for analysis with PLINK. PLINK is a commonly used command-line program that features many statistical methods such as case-control association, various regression methods, permutation test, FDR, and etc. Analysis commands in PLINK are issued and managed through gPLINK, a JAVA-based graphical user interface developed by the same group along with PLINK. gPLINK has been modified and enhanced to better integrate with SNPTrack. Analysis results may be visualized through Haploview. LD and haplotypes in the region around a particular SNP can be downloaded from HapMap and viewed in Haploview. Lists of potentially interesting SNPs can also be saved directly into the SNPTrack StudyDB from Haploview for further interpretation with SNPTrack’s libraries. As development of SNPTrack progresses, this framework for linking external tools will be applied to other standalone analysis tools such as SAS, R/Bioconductor, and Matlab.
- The LIB component is shared by SNPTrack and ArrayTrack™. It is comprised of a number of libraries, with each library containing content-specific information to assist in the interpretation of omics data as well as other genomic and genetic research. The ArrayTrack™ System contains libraries that partially mirror the contents of dbSNP, GenBank, SWISS-PROT, LocusLink, Kyoto Encyclopedia of Genes and Genomes (KEGG), GO and others. The functional information from these databases is extracted to construct several enriched libraries, such as SNPLib, GeneLib, ProteinLib and PathwayLib that, as the names suggest, concentrate functional information on SNPs, genes, proteins and pathways, respectively. With its list-based query and cross-linked libraries, the LIB component is a powerful tool for data interpretation.