Table 2.

Biological process categories overrepresented in intermediate lesions

GO Name	Z-score	P-value
For up-regulated genes
immune response	14.491	0.000
antigen processing, endogenous antigen via MHC class I	3.821	0.014
antigen processing, exogenous antigen via MHC class II	5.968	0.001
cellular defense response	5.669	0.000
cell-mediated immune response	3.093	0.038
T-helper 1 type immune response	3.214	0.035
humoral immune response	9.451	0.000
complement activation	3.608	0.016
inflammatory response	8.515	0.000
neutrophil chemotaxis	6.629	0.004
leukocyte adhesion	4.767	0.013
immune cell activation	3.268	0.011
immune cell migration	6.25	0.000
cell surface receptor linked signal transduction	2.082	0.042
integrin-mediated signaling pathway	2.633	0.035
intracellular signaling cascade	4.367	0.000
MAPKKK cascade	2.413	0.037
myeloid cell differentiation	2.876	0.042
lipid transport	3.255	0.011
Phagocytosis	4.757	0.005
Apoptosis	2.091	0.049
cell proliferation	4.257	0.000
T cell proliferation	5.489	0.003
oxygen transport	3.255	0.016
icosanoid metabolism	3.524	0.010
lipoprotein metabolism	3.291	0.017
For down-regulated genes
cellular catabolism	2.708	0.014
amine catabolism	3.599	0.011
glycine catabolism	8.457	0.003
glycine metabolism	5.817	0.008
ubiquitin cycle	2.092	0.041
protein folding	3.088	0.008
Endocytosis	2.521	0.032

GO analysis was applied to differentially expressed genes in intermediate lesions compared with normal controls. Similar significant categories were not included to reduce redundancy. 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 3]