title: TOM: a web-based integrated approach for identification of candidate disease genes.
abstract: The massive production of biological data by means of highly parallel devices like microarrays for gene expression has paved the way to new possible approaches in molecular genetics. Among them the possibility of inferring biological answers by querying large amounts of expression data. Based on this principle, we present here TOM, a web-based resource for the efficient extraction of candidate genes for hereditary diseases. The service requires the previous knowledge of at least another gene responsible for the disease and the linkage area, or else of two disease associated genetic intervals. The algorithm uses the information stored in public resources, including mapping, expression and functional databases. Given the queries, TOM will select and list one or more candidate genes. This approach allows the geneticist to bypass the costly and time consuming tracing of genetic markers through entire families and might improve the chance of identifying disease genes, particularly for rare diseases. We present here the tool and the results obtained on known benchmark and on hereditary predisposition to familial thyroid cancer. Our algorithm is available at http://www-micrel.deis.unibo.it/~tom/.
authors.affiliation: Functional Genomics Laboratory and Telethon Facility, DAMA Data Mining for Analysis of DNA Microarrays, Dipartimento di Morfologia ed Embriologia, Via Fossato di Mortara 64b, 44100 Ferrara, Italy. simona.rossi@gmail.com
authors.forename: Simona
authors.initials: S
authors.lastname: Rossi
authors.forename: Daniele
authors.initials: D
authors.lastname: Masotti
authors.forename: Christine
authors.initials: C
authors.lastname: Nardini
authors.forename: Elena
authors.initials: E
authors.lastname: Bonora
authors.forename: Giovanni
authors.initials: G
authors.lastname: Romeo
authors.forename: Enrico
authors.initials: E
authors.lastname: Macii
authors.forename: Luca
authors.initials: L
authors.lastname: Benini
authors.forename: Stefano
authors.initials: S
authors.lastname: Volinia
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D020869:Gene Expression Profiling; D030342:Genetic Diseases, Inborn / Q000235:genetics*; D008040:Genetic Linkage; D020022:Genetic Predisposition to Disease; D020407:Internet; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software; D018511:Systems Integration; D013964:Thyroid Neoplasms / Q000235:genetics; D014584:User-Computer Interface