TOM: a web-based integrated approach for identification of candidate disease genes.
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/.
Rossi
Simona
S
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
Masotti
Daniele
D
Nardini
Christine
C
Bonora
Elena
E
Romeo
Giovanni
G
Macii
Enrico
E
Benini
Luca
L
Volinia
Stefano
S
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