Table 5.

Genes whose mRNA or protein expression is altered by treatment with histone deacetylase inhibitors.

Class	Gene list
Histone deacetylase inhibitor-upregulated gene expression
Cell cycle inhibitory gene	p21WAF1, p16INK4A, p27KIP1, GADD45
Tumor suppressor gene	p53, VHL, p107, gelsolin, IGFBP3
Proapoptotic gene	CD95, TRAIL, DR4, DR5, Bax, Bak, Bim, Bmf, Apaf1
Differentiation gene	RARβ2, TGFβ1
Antimetastatic gene	TIMP1, TIMP2, RECK
Immune response gene	MHC-I, MHC-II, CD40, CD80, CD86, ICAM1
Histone deacetylase inhibitor-downregulated gene expression
Cell cycle regulatory gene	Cyclin D1, Cyclin A, thymidylate synthetase, CTP synthase
Antiapoptotic gene	Bcl-2, Bcl-XL, Bcl-w, MCL1, XIAP
DNA repair gene	Ku70, Ku86, DNA-PKcs
Hormone receptor gene	EGFR, ERα, HER2/neu
Metastatic gene	MMP2, MMP9
Signal transduction gene	Akt, Flt-3, Raf-1, Abl
Angiogenic factor gene	HIF1α, VEGF, IL2, IL10, bEGF, TIE2, eNOS, CXCR4