Table 3.

Biological process categories overrepresented in advanced lesions

GO Name	Z-score	P-value
For up-regulated genes
immune response	6.305	0.000
cellular defense response	2.94	0.026
humoral immune response	5.392	0.000
inflammatory response	6.179	0.000
immune cell migration	4.778	0.014
intracellular signaling cascade	4.297	0.001
small GTPase mediated signal transduction	2.372	0.024
I-kappaB kinase/NF-kappaB cascade	6.408	0.000
T cell proliferation	4.186	0.016
induction of apoptosis	3.709	0.007
oxygen transport	4.778	0.003
amine transport	3.051	0.024
anion transport	3.373	0.006
phosphate transport	6.139	0.000
organic acid transport	2.634	0.039
nucleoside monophosphate metabolism	5.853	0.001
cell adhesion	3.958	0.000
For down-regulated genes
response to protein stimulus	6.79	0.000
response to unfolded protein	6.79	0.000
integrin-mediated signaling pathway	4.36	0.003
Apoptosis	2.838	0.003
muscle cell differentiation	3.771	0.032
vasculature development	3.795	0.005
neuron differentiation	3.993	0.003
vitamin transport	3.771	0.023
RNA metabolism	3.476	0.000
RNA splicing	3.497	0.005
glutamine metabolism	4.901	0.004
macromolecule metabolism	2.214	0.023
protein folding	5.643	0.000
cell-matrix adhesion	2.605	0.036
peptide hormone secretion	5.401	0.004

GO analysis was applied to differentially expressed genes in advanced lesions compared with normal controls. Some other selected categories are shown. The first half of the table indicates categories highly significant for up-regulated genes; the second half of the table shows categories highly significant for down-regulated genes. Calculated p-values and Z-scores for each category are shown. The corresponding cell component categories and molecular function categories are available in additional data [see Additional file 6]