A new web-based data mining tool for the identification of candidate genes for human genetic disorders
| Autor: | Patrick Kemmeren, Jack A. M. Leunissen, Han G. Brunner, Koen Cuelenaere, Marc A. van Driel |
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| Jazyk: | angličtina |
| Rok vydání: | 2003 |
| Předmět: |
expression database
Candidate gene ror2 Available expression Bioinformatics adult-syndrome Gene Expression Computational biology Biology dysplasia Databases Genetic human genome Bioinformatica Genetics Web application Humans Genetics (clinical) mouse recessive robinow-syndrome Internet noonan-syndrome business.industry Noonan Syndrome EPS-4 Genetic Diseases Inborn Computational Biology sequence Data warehouse Identification (information) Genetic defects of metabolism [UMCN 5.1] Chromosomal region Human genome The Internet mutation business Databases Nucleic Acid Cellular energy metabolism [UMCN 5.3] Software |
| Zdroj: | European Journal of Human Genetics, 11, 57-63 European Journal of Human Genetics, 11, 1, pp. 57-63 European Journal of Human Genetics 11 (2003) |
| ISSN: | 1018-4813 |
| Popis: | Item does not contain fulltext To identify the gene underlying a human genetic disorder can be difficult and time-consuming. Typically, positional data delimit a chromosomal region that contains between 20 and 200 genes. The choice then lies between sequencing large numbers of genes, or setting priorities by combining positional data with available expression and phenotype data, contained in different internet databases. This process of examining positional candidates for possible functional clues may be performed in many different ways, depending on the investigator's knowledge and experience. Here, we report on a new tool called the GeneSeeker, which gathers and combines positional data and expression/phenotypic data in an automated way from nine different web-based databases. This results in a quick overview of interesting candidate genes in the region of interest. The GeneSeeker system is built in a modular fashion allowing for easy addition or removal of databases if required. Databases are searched directly through the web, which obviates the need for data warehousing. In order to evaluate the GeneSeeker tool, we analysed syndromes with known genesis. For each of 10 syndromes the GeneSeeker programme generated a shortlist that contained a significantly reduced number of candidate genes from the critical region, yet still contained the causative gene. On average, a list of 163 genes based on position alone was reduced to a more manageable list of 22 genes based on position and expression or phenotype information. We are currently expanding the tool by adding other databases. The GeneSeeker is available via the web-interface (http://www.cmbi.kun.nl/GeneSeeker/). |
| Databáze: | OpenAIRE |
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