Gene prioritization refers to a family of computational techniques for inferring disease genes through a set of training genes and carefully chosen similarity criteria. Test genes are scored based on their average similarity to the training set, and the rankings of genes under various similarity criteria are aggregated via statistical methods.
Performs genotype analysis. GeneMarker is an application allowing the analysis of fragments. It includes a set of tools including a size template editor as well as a function to generate size calibration charts. It also provides features for analyzing multiplex ligation-dependent probe amplification (MLPA). This program can be used in conjunction with sequencing systems.
Consists of a one-stop online assembly of computational software tools. ToppGene Suite enables users to (i) perform gene list enrichment analysis, (ii) perform candidate gene prioritization based on functional annotations, (iii) perform candidate gene prioritization based on protein interactions network analysis and (iv) identify and rank candidate genes in the interactome based on both functional annotations and e protein-protein interaction network (PPIN) analysis. The suite can identify true candidate genes.
Assesses the degree of relatedness among genes within disease regions. GRAIL finds a subset of genes and attributes a select set of keywords that suggest putative biological pathways. It takes a list of disease regions and uses an automated text-based strategy to work. This tool can differentiate disease regions from a longer list of results containing a large number of false positive regions. It enables users to genetically validate any individual rare deletion.
Assists in the prioritization of candidate genes. ENDEAVOUR is a web application that consists of (i) inferring several models (based on various genomic data sources), (ii) applying each model to the candidate genes to rank those candidates against the profile of the known genes and (iii) merging the several rankings into a global ranking of the candidate genes.
A tool focusing on discovering genes based on user-specific disease/phenotype terms. Phenolyzer exhibits superior performance over competing methods for prioritizing Mendelian and complex disease genes, based on disease or phenotype terms entered as free text.
A text-mining approach to map relationships between more than 5000 human genetic disease phenotypes from the OMIM database. This interface enables the user to retrieve the similarity ranking for a specific OMIM phenotype.
Permits prioritization of candidate genes associated with human congenital cataract. iSyTE was created using an in silico subtraction approach by which lens microarray data sets are compared to a developmentally matched microarray data set representing the whole embryonic body from which the ocular tissue was removed by microdissection. The tool was used in case of human congenital cataract in which a translocation breakpoint ostensibly responsible for the proband’s phenotype was located within a relatively gene-poor genomic interval.