TABLE 2.

Genes Selected for Use in this Study

Gene symbol	Gene name	Taqman assay ID	Category for inclusion	Genes found expressed (Fig. 4)	Functional selection (Fig. 5)	Ref.
BCL2	B-cell CLL/lymphoma 2	Hs00608023_m1	Antiapoptosis	X	X	Zhan et al. (1994)
LEF1	Lymphoid enhancer-binding factor 1	Hs00212390_m1	Antiapoptosis			Hu et al. (2004)
MCL1	Myeloid cell leukemia sequence 1	Hs00172036_m1	Antiapoptosis	X	X	Hu et al. (2004), Dickinson et al. (2004), and Zhan et al. (1997)
CASP1	Caspase 1	Hs00354836_m1	Apoptosis	X		Islaih et al. (2004)
GZMA	Granzyme A (granzyme 1)	Hs00196206_m1	Apoptosis			Seidel et al. (2004)
GZMB	Granzyme B (granzyme 2)	Hs00188051_m1	Apoptosis			Hu et al. (2004)
AURKA	Aurora kinase A	Hs00269212_m1	Cell cycle	X	X	Muller et al. (2005)
INCENP	Inner centromere protein antigens 135/155 kDa	Hs00220336_m1	Cell cycle	X	X	Hu et al. (2004)
PCNA	Proliferating cell nuclear antigen	Hs00427214_g1	Cell cycle	X		Amundson et al. (2000)
PLK1	Polo-like kinase 1 (Drosophila)	Hs00153444_m1	Cell cycle	X	X	Muller et al. (2005)
SAC3D1	SAC3 domain containing 1	Hs00203282_m1	Cell cycle	X		Amundson et al. (2005)
TOP1	Topoisomerase (DNA) I	Hs00243257_m1	Cell cycle	X		Lee et al. (2003)
TOP2A	Topoisomerase (DNA) II alpha 170 kDa	Hs00172214_m1	Cell cycle	X	X	Hu et al. (2004)
CDKN1C	Cyclin-dependent kinase inhibitor 1C (p57) (Kip2)	Hs00175938_m1	Cell cycle regulation			Dickinson et al. (2004) and Lee et al. (2003)
TOB1	Transducer of ERBB2, 1	Hs00271739_s1	Cell cycle regulation	X		Dickinson et al. (2004)
MAK	Male germ cell-associated kinase	Hs00195446_m1	Cell cycle regulation	X		Hu et al. (2004)
H2AFX	H2A histone family, member X	Hs00266783_s1	Cell cycle, chromatin	X		Muller et al. (2005)
HIST1H1C	Histone 1, H1c	Hs00271185_s1	Cell cycle, chromatin	X	X	Muller et al. (2005)
HIST1H2AC	Histone 1, H2ac	Hs00185909_m1	Cell cycle, chromatin	X		Muller et al. (2005)
MATR3	Matrin 3	Hs00251579_m1	Cell cycle, nucleus	X		Islaih et al. (2004)
ACTB	Beta actin	Hs99999903_m1	Cytoskelet	X		Hu et al. (2004)
XPC	Xeroderma pigmentosum complementation group C	Hs00190295_m1	DNA repair	X	X	Amundson et al. (2000)
VAMP3	Vesicle-associated membrane protein 3 (cellubrevin)	Hs00608325_m1	Exo/endocytosis, inflammatory response	X		Islaih et al. (2004)
IL1B	Interleukin 1 beta	Hs00174097_m1	Inflammatory response	X		Amundson et al. (2000)
NDUFA1	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 1, 7.5 kDa	Hs00244980_m1	Mitochondrial function	X		Hu et al. (2004)
APEX1	APEX nuclease (multifunctional DNA repair enzyme) 1	Hs00172396_m1	oxidative DNA damage response	X		Fritz et al. (2003)
G3BP2	GTPase activating protein (SH3 domain) binding protein 2	Hs00367030_m1	p53 regulation			Hu et al. (2004)
CCNG1	Cyclin G1	Hs00171112_m1	p53 target gene			Amundson et al. (2000)
CDKN1A	Cyclin-dependent kinase inhibitor 1A (p21) (Cip1)	Hs00355782_m1	p53 target gene	X	X	Amundson et al. (2000)
DDIT3	DNA damage inducible transcript 3	Hs00358796_g1	p53 target gene	X	X	Holbrook et al. (1996)
MDM2	Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse)	Hs00242813_m1	p53 target gene	X	X	Amundson et al. (2003)
PHLDA3	Pleckstrin homology-like domain, family A, member 3	Hs00385313_m1	p53 target gene	X	X	Amundson et al. (2005)
PPM1D	Protein phosphatase 1D magnesium-dependent, delta isoform	Hs00186230_m1	p53 target gene	X	X	Amundson et al. (2005)
TP53I3	Tumor protein p53 inducible protein 3	Hs00153280_m1	p53 target gene	X	X	Islaih et al. (2004)
BAX	BCL2-associated X protein	Hs00180269_m1	p53 target gene, apoptosis	X		Zhan et al. (1997)
ATF3	Activating transcription factor 3	Hs00231069_m1	Stress response	X	X	Fan et al. (2002)
cFOS	v-fos FBJ murine osteosarcoma viral oncogene homolog	Hs00170630_m1	Stress response	X	X	Dickinson et al. (2004), Holbrook et al. (1996), and Hollander et al. (1993)
GADD45A	Growth arrest and DNA damage inducible, alpha	Hs00169255_m1	Stress response	X	X	Dickinson et al. (2004), Amundson et al. (2000), and Holbrook et al. (1996)
GADD45B	Growth arrest and DNA damage inducible, beta	Hs00169587_m1	Stress response	X		Dickinson et al. (2004)
GADD45G	Growth arrest and DNA damage inducible, gamma	Hs00198672_m1	Stress response			Dickinson et al. (2004)
GSTA2	Glutathione S-transferase A2	Hs00747232_mH	Stress response			Aubrecht et al. (1999), Rushmore and Pickett (1990), and Todd et al. (1995)
HERPUD1	Homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1	Hs00206652_m1	Stress response	X		Muller et al. (2005)
JunB	jun B proto-oncogene	Hs00357891_s1	Stress response	X		Dickinson et al. (2004) and Holbrook et al. (1996)
DNAJB1	DnaJ (Hsp40) homolog, subfamily B, member 1	Hs00428680_m1	Stress response/Protein folding	X		Hu et al. (2004) and Dickinson et al. (2004)
HSPA14	Heat shock 70-kDa protein 14	Hs00212495_m1	Stress response/Protein folding	X		Todd et al. (1995) and Mosser et al. (1988)
HSPA5	Heat shock 70-kDa protein 5 (glucose-regulated protein, 78kDa)	Hs00607129_gH	Stress response/Protein folding	X		Todd et al. (1995) and Wooden et al. (1991)
EIF1	Eukaryotic translation initiation factor 1	Hs00603727_g1	Stress response/Protein synthesis	X		Sheikh et al. (1999)
GDF15	Growth differentiation factor 15	Hs00171132_m1	Survival factor/p53 target gene	X	X	Islaih et al. (2004)

Note. Gene symbols and corresponding Taqman Assay IDs of the genes selected for this study are listed in the first and second column, respectively. Further annotations given are the official gene name(s) and additional aliases, if available. Column 4 mentions the category deduced from the function or the known expression regulation of the genes which was considered during initial gene selection. Column 5 indicates the genes found expressed and appearing in the heat map in Figure 4, whereas column 6 specifies the functional gene selection shown in the heat maps of Figure 5.