Prioritization of candidate cancer genes--an aid to oncogenomic studies.
The development of techniques for oncogenomic analyses such as array comparative genomic hybridization, messenger RNA expression arrays and mutational screens have come to the fore in modern cancer research. Studies utilizing these techniques are able to highlight panels of genes that are altered in cancer. However, these candidate cancer genes must then be scrutinized to reveal whether they contribute to oncogenesis or are coincidental and non-causative. We present a computational method for the prioritization of candidate (i) proto-oncogenes and (ii) tumour suppressor genes from oncogenomic experiments. We constructed computational classifiers using different combinations of sequence and functional data including sequence conservation, protein domains and interactions, and regulatory data. We found that these classifiers are able to distinguish between known cancer genes and other human genes. Furthermore, the classifiers also discriminate candidate cancer genes from a recent mutational screen from other human genes. We provide a web-based facility through which cancer biologists may access our results and we propose computational cancer gene classification as a useful method of prioritizing candidate cancer genes identified in oncogenomic studies.
Furney
Simon J
SJ
Research Unit on Biomedical Informatics, Experimental and Health Science Department, Universitat Pompeu Fabra, Barcelona 08080, Spain.
Calvo
Borja
B
Larrañaga
Pedro
P
Lozano
Jose A
JA
Lopez-Bigas
Nuria
N
D000818:Animals; D002965:Classification / Q000379:methods; D019295:Computational Biology / Q000379:methods*; D004252:DNA Mutational Analysis; D016147:Genes, Tumor Suppressor; D023281:Genomics / Q000379:methods*; D006801:Humans; D011519:Proto-Oncogenes