Table 3.

Autophagy pathway and genes listed by RT2 Profiler PCR Arrays-Mouse Autophagy.

Autophagy Machinery Components
Autophagic Vacuole Formation:	Atg4b, Atg4c, Atg9a, Gabarap, Gabarapl1, Gabarapl2, Wipi1, Becn1, Ulk1, Map1lc3
Ubiquitination and phagophore expansion:	Atg12, Atg16l1, Atg16l2, Atg3, Atg5, Atg7, Hdac6, Map1lc3a
Vacuole targeting and autophagosome-lysosome Linkage	Lamp1, Npc1, Gabarap, Atg4b, Atg4c
Chaperone-mediated autophagy	Hsp90aa1, Hspa8
Regulation of Autophagy
Co-Regulators of autophagy and apoptosis	Dram1, Akt1, App, Atg12, Atg5, Bad, Bak1, Bax, Bcl2, Bcl2l1 (BclXL), Becn1,Bid, Bnip3, Casp3, Casp8 (FLICE), Cdkn1b (p27Kip1), Cdkn2a (p16INK4a), Cln3, Ctsb, Cxcr4, Dapk1, Eif2ak3, Fadd, Fas(Tnfrsf6), Hdac1, Htt, Ifng, Igf1, Ins2, Mapk8 (JNK1), Mtor, Nfkb1, Pik3cg, Prkaa1 (Ampk), Pten, Snca, Sqstm1, Tgfb1, Tgm2,Tnf, Tnfsf10 (Trail), Trp53 (p53).
Co-Regulators of autophagy and the cell cycle	Bax, Cdkn1b (p27Kip1), Cdkn2a (p16INK4a), Ifng, Pten, Rb1, Tgfb1, Trp53 (p53).
Autophagy induction by intracellular pathogens	Eif2ak3, Ifng, Lamp1.
Autophagy in response to other intracellular signals	Ctsd, Ctss, Dram2 (Tmem77), Eif4g1, Esr1 (Erα), Gaa, Hgs, Mapk14(p38alpha), Pik3c3 (Vps34), Pik3r4, Rps6kb1, Tmem74, Ulk2, Uvrag.