Phenotype Genotype Mapper (PGMapper)

Category Genomics>Genetic Data Analysis/Tools

Abstract PGMapper is a web-based software tool for linking phenotype to genes.

It can be used for automatically matching a phenotype to genes from a defined 'genome region' or a 'group of given genes' by combining the mapping information from the Ensembl database and 'gene function' information from the Online Mendelian Inheritance in Man (OMIM) and PubMed databases.

Candidate ‘gene search’ can be based on the genome region and key words that describe the particular phenotypic features specified by the end-users.

PGMapper obtains the information of all genes of a disease locus or quantitative trait loci (QTL) from the Ensembl database and then searches the OMIM and PubMed to find those genes relevant to a disease or a phenotype trait according to known literature reports.

For all candidate genes, PGMapper provides detailed information of the gene(s) and all related references that support the candidacy in the OMIM and PubMed databases.

It also allows users to easily construct complex search strategies using different combinations of keywords or phrases, field qualifiers, text connectors and Boolean operators and to test a variety of possible relationships between genes and phenotypic traits.

Although PGMapper was developed to identify the candidate genes of a QTL or a disease locus, it can also be used for 'whole genome analysis' of a complex trait or a disease.

PGMapper is a web application based on Java technologies.

The interface of the system is user friendly and interactive, and all results can be viewed online or saved in Excel or the portable document format (PDF) format for further analysis.

PGMapper 'QTL module' and 'disease locus' module --

The QTL module and disease locus module are both developed to search candidate genes for QTL and disease loci, respectively.

The inputs to the system are the map location of a QTL or a disease locus and keywords that can describe the features of a particular phenotypic trait or disease.

First, PGMapper retrieves the information of all genes within a QTL or a disease locus from the Ensembl database and then it searches both OMIM and PubMed to obtain information about candidate genes.

The 'search term' is the combination of the ‘gene symbol’ and the keywords related to the phenotype.

For each candidate, all references found from OMIM or PubMed are listed on a separate page.

Users can follow the link to see more details for each reference.

PGMapper Microarray module --

Microarray module is used to search candidate genes for microarray experiments.

Users may first choose a set of 'differentially expressed' genes between the ‘experimental group’ and the ‘control group’ or those ‘genes of interest’, as the inputs to the system and then specify the key words possibly associated with specific disease phenotypes.

The system will automatically pick out those genes that may have actions on a disease or other traits of interest based on all available reports in both OMIM and PubMed.

Note: PGMapper is currently available for the candidate gene search of human, mouse, rat, zebra fish and 12 other species.

System Requirements

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Manufacturer

Manufacturer Web Site PGMapper

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G6G Abstract Number 20477

G6G Manufacturer Number 104102