The columns of information in the calculation files are as follows:

1. Cell cycle phase.

2. Functional category.

• DNA damage induced or repressed genes are regarded as a category here.
• UV – ultraviolet light; MMS – methyl methane sulfonate; E7 – transfection with the E7 oncoprotein (not discussed in article)
• “UP” refers to induction; “DOWN” refers to repression.

3. Number of probe sets of Affx chip.

4. Number of genes in the cell cycle phase.

5. Number of genes that fall into the given functional category.

6. Number of genes from columns 4 and 5 expected to overlap based on random chance.

7. Number of genes from columns 4 and 5 that are observed to overlap.

8. Whether number of genes in column 7 is OVER-represented or UNDER-represented from what was expected based on chance alone.

9. p-value based on binomial distribution of whether the number of genes in column 7 is consistent with number of genes based on random chance (column 6).