We hypothesized their roles in radiosensitivity using gene set analysis and pathway analysis. Results Selection of a common radiosensitivity signature from four microarray platforms The study design is in Figure 1. Four published micro array experiments were reanalyzed to identify genes whose expression correlated with radiosensitivity in NCI 60 cancer cell lines. The SF2 radiosensitivity all targets index was determined from previously published literature and considered as a continuous variable ranging from 0 to 1. For gene selection, significant analysis of microarrays was applied at the false discovery rate of 0. 10. This resulted in 31 genes commonly identified regardless of platforms and 179 selected from more than three platforms.

Differ ences in gene expression between definitely radiosensi tive and radioresistant cells by principal component analysis showed that approximately the top 10% of radiosensitive cell lines were distinguished from the bottom 10% of radioresistant lines using the 31 signature genes. Of these genes, 21 genes were downregulated and 10 were upregulated in radiosensitive cell lines. Reduced expression in a radiosensitive cells meant that decreased gene ex pression was observed in radiosensitive cells relative to radioresistant cells. Likewise, upregulation meant increased gene expression in radiosensitive cells relative to radioresistant cells. This was determined as the slope of the correlation coefficient between SF2 and gene ex pression. The scatter plots showing relationships be tween SF2 and gene expression of the 31 radiosensitivity signature genes in the four microarrays are in Additional files 2, 3, 4, and 5.

Integrative functional gene set analysis using a global test To explain the biological processes and signaling path ways of radiosensitivity, a gene set functional study using a global test was applied. The selected gene set was defined from the Kyoto encyclopedia of genes and gen omes pathways. The adjusted p value corrected for multiple comparisons using the Benjamini and Hochberg method is in Table 2. Several radiation related functions were enriched including the cell cycle, DNA replication, cell junction, and cell adhesion.

In addition, several molecular pathways were overrepresented including the integrin, vascular endo thelial growth factor, mitogen activated protein Genetic network interaction with adhesion related molecules in the integrin signaling pathway To generate a genetic network for radiosensitivity, we performed ontology analysis using 179 genes that were selected from more than three platforms using SAM ana lysis. Statistical ranking with canonical pathways was per formed using AV-951 ingenuity pathway analysis . Overrepresented pathways were adhesion related pathways including the integrin, actin cytoskel eton, and focal adhesion kinase signaling pathway. In addition, the cell cycle and p53 signaling pathways important to radiosensitivity were also identified.