Table 1.
Over-represented biological functions of CUX1 targets
| Function | Background (%) | Targets (%) | P-value |
|---|---|---|---|
| Mitotic cell cycle | 2.6 | 4.9 | 2.12E-10 |
| DNA replication and chromosome cycle | 1.5 | 3.0 | 3.46E-08 |
| Cell cycle | 5.6 | 8.3 | 4.18E-08 |
| Cell proliferation | 8.5 | 11.6 | 8.83E-08 |
| M phase of mitotic cell cycle | 1.0 | 2.3 | 9.66E-08 |
| Mitosis | 1.0 | 2.2 | 1.65E-07 |
| M phase | 1.3 | 2.6 | 3.57E-07 |
| DNA replication | 1.1 | 2.3 | 1.44E-06 |
| Nuclear division | 1.3 | 2.5 | 1.90E-06 |
| S phase of mitotic cell cycle | 1.2 | 2.3 | 2.24E-06 |
| DNA metabolism | 4.2 | 6.3 | 2.37E-06 |
| Cell growth and/or maintenance | 30.3 | 34.0 | 7.61E-05 |
| Intracellular transport | 4.5 | 6.1 | 0.00044 |
| Nucleosome assembly | 0.5 | 1.1 | 0.00049 |
| Protein metabolism | 19.9 | 22.6 | 0.00061 |
| DNA-dependent DNA replication | 0.6 | 1.2 | 0.00074 |
| Cell cycle checkpoint | 0.3 | 0.7 | 0.00079 |
| Regulation of cell cycle | 3.1 | 4.3 | 0.00090 |
| Small GTPase mediated signal transduction | 1.9 | 2.8 | 0.00110 |
| Protein folding | 1.0 | 1.7 | 0.00186 |
A single list of putative targets of CUX1 was compiled from eight individual ChIP–chip experiments from cell lines overexpressing p110 CUX1. Genes that were bound by CUX1 (Targets) were compared with all genes present on the microarray (Background) by using a web-based functional annotation tool, DAVID. Overrepresentation of a function depends on the increase in the proportion of genes involved in a given function between CUX1 targets and the background. The P-value is determined using an improved Fisher's exact test from the DAVID software (40). The top 20 significantly over-represented functions are shown.