Expression quantitative trait loci (eQTLs) are genetic variants that affect gene expression. eQTL mapping is done using standard qtl mapping methods that test the linkage between variation in expression and genetic polymorphisms. eQTL analysis software tools use different approaches and algorithms to analyze eQTL from RNA-seq or microarray experiments.
A quantitative trait loci (QTL) mapping method guided by prior knowledge for identifying candidate genes. Lasso includes three steps: i) identifying QTLs from QTL mapping; ii) generating and selecting gene modules; iii) prior knowledge guided QTL mapping. Lasso also can find the robust gene modules significantly associated with traits and SNP markers simultaneously. In addition, Lasso is a method applicable for different experimental design and a variety of species.
Allows execution and comparison of a variety of modern QTL-mapping methods and supports third-party addition of new ones. QGene accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable.
A platform of database and web services designed for data integration, analysis and visualization of SNP-gene associations in eQTL (expression quantitative trait loci) studies. With its interactive user interface and client-server platform, Genevar allows researchers to instantly investigate eQTL association patterns within a genetic region of interest.
A software tool for computationally efficient eQTL analysis. Matrix eQTL supports additive linear and ANOVA models with covariates, including models with correlated and heteroskedastic errors. The issue of multiple testing is addressed by calculating false discovery rate; this can be done separately for cis- and trans-eQTLs.
Provides an online platform for collecting, managing, analyzing, visualizing and sharing large and complex biomedical data sets. MOLGENIS Research is a life science data solution built on top of the MOLGENIS platform. It integrates apps to inspect, organize, and customize the data. Moreover, it allows the development of various apps for specific tasks, as well as uploading of data models and settings making the platform suitable for specific uses.
Represents novel functional sites with DNA-level variation relevant to many human phenotypes and health. The eqtl.uchicago.edu is a web browser to both summarize the results of these studies and to allow for quick and easy comparisons across studies. This method is meant to be searchable based on genome coordinates, gene name, and single nucleotide polymorphism (SNP) identifier.
An expression quantitative trait locus (eQTL) represents a marker (locus) in the genome in which variation between individuals is associated with a quantitative gene expression trait, often measured as mRNA abundance. Thus, the three critical components to eQTL results are 1) the genotypes at a marker (here a SNP), 2) the gene expression levels, as measured by a probe or sequence information, and 3) a measure of the statistical association between the two in a study population, such as the p-value. The eQTL browser provides a means to query a database of eQTL results, applying filters based on the above types of data. It should be recognized that a substantial number of tests are performed, and that the significance of p-values should be considered in this multiple testing context.