Table 3. Cellular functions significantly up-regulated in MBP induced EAE in the Lewis rat.

Function	Prediction	No of genes in direction of prediction	Z score	Overlap p-value	Genes for which expression direction predicts an increase in function*	Genes for which expression direction predicts a decrease in function	Genes which affect the function
Activation of central nervous system cells	Increased	9 of 12	2.268	2.83E–03	Il1b,Gfap, Ptgs2, Vim, Il1rn, Cebpb, Tlr2, Tlr4, Npc1	Kcnj10,Ace	Gjd2
Activation of astrocytes	Increased	9 of 10	2.595	1.55E–03	Il1b,Gfap, Ptgs2, Vim, Il1rn, Cebpb, Tlr2, Tlr4, Npc1	Kcnj10,Ace
Apoptosis of leukocytes	Increased	82 of 136	2.328	2.06–06	Tnfrsf1a, Fas, Irf1, Myd88, Lcn2, Tlr2, Tlr4, Stat1	Irgm	Casp3, Casp4
Apoptosis of microglia	Increased	7 of 9	2.570	1.08–06	Fas, Irf1, Myd88, Lcn2, Tlr2, Tlr4, Stat1	Casp3, Casp4
Cell death of dopaminergic neurons	Increased	10 of 13	2.071	4.94E–04	Park2, Ppargc1a, TRB@, Cd4, Casp7, Casp8 , Lep , Casp3, Shh, Mapk8ip1,	Snca , Cybb ,	Fas
Formation of amyloid fibrils	Increased	5 of 6	2.213	4.55E–03	Tnfrsf1a , Mme, Apoe, Apba2, Sod2		Psen1
Proliferation of oligodendrocyte precursor cells	Increased	5 of 5	2.236	7.83E–03	Cxcl2, Rps6kb2 , Thrb, Igf1 , Plp1

^* Gene abbreviations are given in Tables S1 and S2. Gene names in Bold indicate increased expression in EAE, normal italic font indicates decreased expression.