Category Genomics>Genetic Data Analysis/Tools

Abstract GeneDistiller is a web-based application that provides knowledge-driven, fully interactive and intuitive access to multiple data sources.

It displays maximum relevant information, while saving the user from drowning in the flood of data.

A typical query takes less than two (2) seconds, thus allowing an interactive and explorative approach to the hunt for the candidate gene.

Information from various data sources such as gene-phenotype associations, 'gene expression patterns' and protein-protein interactions were integrated into a central database.

Researchers can select which information for the genes within a candidate interval or for single genes, shall be displayed.

Genes can also be interactively filtered, sorted and prioritized according to criteria derived from the background knowledge and preconception of the disease under scrutiny.

GeneDistiller is aimed at various strategies --

It can either be used as a tool to query, select and project genes from within a 'linkage interval' together with gene specific data or to display rich information on human candidate genes obtained with other prioritization tools or of the researcher's interest.

Besides this, it offers a customizable user-driven prioritization process integrating the available data as specified by the researcher.

The application features an intuitive interface which enables the researcher to formulate simple queries without the need to read the software manual ahead of time, yet allowing more complex queries.

The software returns all results on one (1) Hypertext Markup Language (HTML) page which can easily be printed or saved.

The kind of information included is determined by the researcher.

Since the results of a search are presented on the fly, the software offers a high degree of interactivity, allowing the researcher to quickly change some parameters to follow new ideas which may arise when reading the results.

You can thus explore the data with the help of the computer and combine newly gained insights with your personal background knowledge.

Strategies --

GeneDistiller offers different approaches to determine the most likely candidate genes:

Projection --

GeneDistiller can list all genes within a ‘linkage interval’ together with gene specific information. Among the different kinds of gene specific data, the researcher can select those relevant to them and print and read this information for all ‘positional candidates’ to choose the most promising gene.

This approach can be very helpful if you only have a vague idea of the disease causing gene.

Selection --

The researcher can apply filters to the genes in the linkage interval, thus narrowing down their number to a small group of more promising candidates.

This approach should be applied when the researcher is able to define conditions that must be fulfilled by the candidate gene, e.g. expression in a certain tissue or co-expression with another gene.

Alternatively, “visual” filters can be used to highlight gene properties so that No gene will be excluded.

Sorting --

Genes can be sorted according to certain parameters, e.g. their position, tissue specific expression or likelihood to encode mitochondrial proteins.

Prioritization --

GeneDistiller offers a user-driven prioritization function which ranks genes according to the researcher's specifications.

Prioritization approaches should be used when the researcher canNot exclude any gene in advance but wants to focus on the genes in falling order of “apparent” relevance.

The user is free to combine these methods to follow a strategy which best suits the problem, e.g. you can exclude genes using filters, choose the parameters to be used in the prioritization process, select those to be displayed in the output and highlight interesting properties.

Application of the different strategies --

While some researchers prefer to read the available information for all genes within a candidate interval, others may rather narrow down the number of genes beforehand and focus on those fulfilling certain conditions that are regarded as mandatory.

Database schema and contents --

The GeneDistiller database stores data from various sources that are most frequently considered by researchers when manually searching for candidate genes.

All gene-specific data is stored in ‘satellite tables’ connected to a central database table GENES in which the genes are defined. These connections are either modeled as 1:1, 1:n or m:n relations, depending on the nature of the data.

The database schema therefore resembles the query-optimized star schema found in many data warehouses (the database schema can be found on the GeneDistiller's website).

GeneDistiller includes the following data: Genes, gene positions, gene RIFs, gene ontology (GO), cellular localization of gene products, transcripts, exons, OMIM reports, mouse phenotypes, protein-protein interactions, gene expression data, protein domains, SNP markers, and STR markers.

Interface --

GeneDistiller is web-based; all interfaces are ordinary HTML pages without any Java applications to be installed.

In the query interface, parameters are grouped into distinct blocks.

Some more advanced parameters such as 'tissue-specific expression' are Not shown by default but all blocks can be switched on and off at the researcher's will.

Output --

GeneDistiller prints the results of a query in HTML format. The resulting page does Not make use of color unless to highlight keywords chosen by the user.

The genes are presented together with all the desired data in an order specified by the researcher and visually separated to increase readability.

The page also includes hyperlinks to the original data to simplify access to more detailed data which might exist on the website of the data source.

Note: At present, GeneDistiller only offers information about human genes. The manufacturer is currently integrating mouse data, as mice are often used as a model organism in gene hunting.

Depending on the use of GeneDistiller by the community and suggestions from the users, other species, especially rat, might be added in the future.

System Requirements



Manufacturer Web Site GeneDistiller

Price Contact manufacturer.

G6G Abstract Number 20429

G6G Manufacturer Number 104057