Table 1.

Overrepresented functional classes among genes significantly regulated by MA in MADR selected lines.

Gene	Name	Apop	Immu	Cyto	Toll	Erbb	Oxid	Ster	MAHDR	MALDR	Saline
Clcf1	Cardiotrophin-like cytokine factor 1	•		•						↓	L
Ripk1	Receptor (TNFRSF)-interacting serine-threonine kinase 1	•			•					↓
Lta	Lymphotoxin A (aka TNF-beta)	•	•	•						↓
Pawr	PRKC, apoptosis, WT1, regulator	•	•							↓
Hspa5	Heat shock 70kD protein 5	•							↑	↑
Il6	Interleukin 6	•	•	•	•	•			↓
Atf5	Activating transcription factor 5	•								↓
Casp8	Caspase 8	•			•				↓
Il2rb	Interleukin 2 receptor, beta chain	•		•						↓
Gzmb	Granzyme B	•								↓
Fas	Fas (TNF receptor superfamily member 6)	•	•	•						↓
Atm	Ataxia telangiectasia mutated homolog	•								↓
Bcl2	B-cell leukemia/lymphoma 2	•								↓	L
H2-Ea	Histocompatibility 2, class II antigen E alpha		•							↓	L
Tgfb1	Transforming growth factor, beta 1		•	•						↓
Ccl2	Chemokine (C-C motif) ligand 2		•	•						↓
Ccl3	Chemokine (C-C motif) ligand 3 (aka MIP-1alpha)		•	•	•					↓
Nfkb2	Nuclear factor of kappa enhancer in B-cells (p52/p100)		•		•				↑	↓
Il1rn	Interleukin 1 receptor antagonist		•							↓
Egfr	Epidermal growth factor receptor			•		•			↑
Mapk3	Mitogen-activated protein kinase 3 (aka Erk-1)				•	•			↓
Fos	FBJ osteosarcoma oncogene (aka AP-1)				•				↑
Esr1	Estrogen receptor 1 (alpha)					•		•		↓
Erbb3	V-erb-b2 erythroblastic leukemia viral oncogene homolog 3					•			↑
Ptgs2	Prostaglandin-endoperoxide synthase 2 (aka Cox-2)						•		↓
Atp5c1	ATP synthase, H+ transporting, mitochondrial F1 complex						•		↓
Ndufs8	NADH dehydrogenase (ubiquinone) Fe-S protein 8						•		↓
Uqcrc2	Ubiquinol cytochrome c reductase core protein 2						•		↓
Atp5g3	ATP synthase, H+ transporting, mitochondrial F0 complex						•		↓
Atp5j	ATP synthase, H+ transporting, mitochondrial F0 complex						•				L
Esr2	Estrogen receptor 2 (beta)							•	↑
Thra	Thyroid hormone receptor alpha							•		↓
Ar	Androgen receptor							•	↑

Arrows in the columns labeled ‘MAHDR’ and ‘MALDR’ indicate the direction of regulation of each gene in response to MA. The column labeled ‘Saline’ indicates which line, if any, showed higher expression of the gene in a drug-naïve state (H = MAHDR; L = MALDR). Overrepresented functional groups were identified using the DAVID Bioinformatics Resources (david.niaid.nih.gov; Huang et al., 2007). The 384 genes represented on the qPCR array were used as the background gene list for pathway analysis. Significance levels for each class: Apoptosis (Apop) p = 0.04; Immune response (Immu) p = 0.0013; Cytokine receptor interaction (Cyto) p = 0.0011; Toll-like receptor signaling pathway (Toll) p = 0.019; ERBB2 signaling pathway p = 0.061; Oxidative phosphorylation (Oxid) p = 0.0097; Steroid hormone receptors (Ster) p = 0.018.