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Gene Function and Pathway Databases – GFuncPathdb


 

Introduction

 

The new website for the Intellectual Disability and Chromosome 21 Genetic Function and Pathway databases can be found here:  http://gfuncpathdb.ucdenver.edu/iddrc/iddrc/GeneQuest.php

 

Intellectual Disability (ID) GFuncPathdb

 Online Mendelian Inheritance in Man (OMIM; www.ncbi.nlm.nih.gov/sites/entrez?db=OMIM) currently lists more than 300 genes that, when mutated, can result in ID. This number may continue to increase as novel gene mutations are reported. More recently, ID has been associated with some cases of genomic copy number variation (CNV); as the extent of the genomic regions are defined, new ID candidate genes may be identified based on gene dosage sensitivity.

 The ID GFuncPath database is designed to provide integrated information on known and candidate ID genes, and their protein features, protein interactions and associated pathways. The goal is to aid both basic science and clinical researchers in new ID gene knowledge discovery and to facilitate hypothesis generation in the molecular basis of ID. The database is searchable by gene name, disease name, genomic location, among other features. Sample query types include:
- is gene X a known ID gene? if so, what disease is it associated with, what are the known mutations, and is ID a primary or secondary feature of the disease?
- what are the protein interaction partners of the gene X protein product? are any of these known ID genes?
- given the genomic coordinates of a specific patient’s CNV, are there any ID genes within the region? If not, what are the protein interaction pathways that lead from genes within the CNV to ID genes?

 

Chromosome 21 (chr21) and Down syndrome (DS) GFuncPathdb

 Down syndrome is the most common genetic cause of intellectual disability. The complete phenotype is both complex, affecting multiple organs and organ systems, and highly variable in severity among individuals. Down syndrome is due to an extra copy of all or part of a normal chromosome 21 and the increased expression, due to gene dosage, of the normal genes encoded by it.

  The large number of genes involved (>500), their functions and interactions, and the perturbations of cellular pathways and processes their increased expression causes, are challenges in determining gene-phenotype correlations.

  The Chr21 GFuncPath database and associated knowledge discovery tools are designed for researchers interested in individual chromosome 21 genes, groups of genes, their orthologs in models organisms, as well as Down syndrome and mouse models of Down syndrome.

  The goal of the database is to facilitate research on human chromosome 21 and Down syndrome, and in this way, facilitate the development of therapeutics for the prevention or amelioration of phenotypic features. The approach is to:
- provide curated, annotated comprehensive information on chromosome 21 genes
- reduce redundant efforts in database and literature searches
- provide links to primary data sources for user evaluation
- provide new tools for data mining
- develop pathway annotation for chr21 proteins

Contact the Colorado IDDRC

Phone: 303-724-3839 • Fax: 303-724-3838

Mailing Address: Mail Stop 8313, 12800 E. 19th Avenue • Aurora, CO 80045

E-mail: Peds.IDDRC@ucdenver.edu

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