Identification of eight candidate target genes of the prognsotic 3p loss in cervical cancer by integrative genomic profiling

We performed integrative gene dosage and expression profiling to identify candidate target genes of the prognostic 3p loss in cervical cancer. Candidate target genes were proposed from the correlation between gene dosage and gene expression. Combined network, gene set, and gene ontology analysis of the gene expression profiles depicted interaction partners of the candidate targets and proposed biological processes that were affected by the 3p loss. Gene dosages from array CGH data (previously submiited to ArrayExpress) were correlated with Illumina gene expression data in the integrative patient cohort. The prognostic significance of the candidate target genes was validated based on the Illumina gene expression data of the validation cohort. Changes in gene expressions after knockdown of three candidate targets, RYBP, TMF1 and PSMD6, were studied by Illumina beadarrays in the cervical cancer cell lines HeLa, SiHa and CaSki.