GCTA (Genome-wide Complex Trait Analysis) is designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits
OmicKriging is a method which emphasizes the use of a wide variety of systems-level data, such as those increasingly made available by comprehensive surveys of the genome, transcriptome and epigenome, for complex trait prediction.
TF-Cluster can be used to identify a set of transcription factors (TFs) controlling a biological process of interest from gene expression data. Its high accuracy in recognizing true positive TFs involved in a biological process makes it extremely valuable in building core GRNs controlling a biological process.
Camelot (CAusal Modeling with Expression Linkage for cOmplex Traits) is a statistical method that integrates genotype, gene expression and phenotype data to automatically build models that both predict complex quantitative phenotypes and identify genes that actively influence these traits.
GeneLink is a data management system designed to facilitate genetic studies of complex traits.In contrast to gene-mapping studies of simple Mendelian disorders, genetic analyses of complex traits are far more challenging, and high quality data-management systems are often critical to the success of these projects. For this reason, we have developed GeneLink, a Web-accessible, password-protected Sybase database that enables genotypic data to be merged easily with pedigree and extensive phenotypic data. GeneLink was designed specifically to facilitate large-scale (multi-center), genetic linkage or association studies and is a powerful tool for complex trait mapping. GeneLink securely and efficiently handles large amounts of data, as well as provides additional features to facilitate quality control and analysis of data generated. In particular, chromosome-specific data files containing marker data in genetic map order can be downloaded in various formats appropriate for downstream analyses (e.g. GAS, LINKAGE). Furthermore, an unlimited number of phenotypes (either qualitative or quantitative) can be stored and analyzed. Finally, GeneLink generates several quality assurance reports, including genotyping success rates of specified DNA samples or success and heterozygosity rates for specified markers. GeneLink has already proven an invaluable tool for complex trait mapping studies and is discussed primarily in the context of our large, multi-center study of hereditary prostate cancer (HPC).
Gillanders, E.M., Masiello, A., Gildea, D., Umayam, L., Duggal, P., Klein, A., Jones, M., Freas-Lutz, D., Ibay, G., Trout, K., Wolfsberg, T.G., Trent, J.M., Bailey-Wilson, J.E., Baxevanis, A.D. 2004. GeneLink: A Database to Facilitate Genetic Studies of Complex Traits.
BMC Genomics 5(1):81.
