Table 1.

Overview of system wide gene expression studies in replicatively aging yeast.

Publications covering either transcriptomes (first 8 rows) or proteome (last row) of wild-type aging yeast. General terms of increasing or decreasing changes are taken as described in the original publications. *Ages inferred from hours of cultivation, assuming a two-hour division time. Color code and superscripts associate changes reported in yeast relative to the hallmarks of human aging as seen in Figure 1 and described in the text; ‘G’ genomic instability, ‘E’ epigenetic alterations , ‘P’ loss of proteostasis , ‘D’ deregulated nutrient sensing , ‘M’ mitochondrial dysfunction .

Publication	Time points	Replicative Ages	Increased Expression	Decreased Expression
Lin et al. 2001 12	2	0; 7-8	Gluconeogenesis D, energy storage D	Glycolysis D
Lesur et al. 2004 9	2	0; 18	Gluconeogenesis D, glyoxylate cycle , lipid metabolism, glycogen production D, stress response (from DNA damage signature set) G	Ribosomes
Koc et al. 2004 11	3	0; 8–12; 8-24	Transport related genes	Glycolysis D, and protein synthesis, folding (chaperones), and degradation (proteasome subunits) P
Laun et al. 2005 8	2	0; 15 (senescent)	DNA damage response (dsDNA break repair) G, cellular stress response, mitochondrial components M, lipid metabolism, cell wall restructuring.
Yiu et al. 2008 13	4	0; 8; 12;18-20	Aerobic metabolism, environmental stress response, nucleotide excision repair, regulatory subunits of Glc7	Ribosomes, nucleolus, methylation related metabolism
Hu et al. 2014 10	2	0; 26-30	All transcripts increased on average 1.3 fold due to loss of silencing, especially transposable elements and genes in rDNA locus E	H3 histone (protein level)
Kamei et al. 2014 14	4	1; 4; 7; 11	Sugar metabolism D, TCA cycle D, amino acid degradation	Amino acid biosynthetic pathways
Janssens & Meinema et al. 2015; transcriptome 7	12	4; 5; 7; 9; 11; 13; 16; 19; 23; 27; 31; 36 *	Gene products integral to membrane, cell wall, sporulation, sterol biosynthesis, stress response (general)	Mitochondria (translation and respiration) M, amino acid biosynthesis, retrotransposons, translation regulation, ribosomes, polarized growth, cortical actin cytoskeleton, ATP/GTP binding, tRNA synthesis
Janssens & Meinema et al. 2015; proteome 7	12	4; 5; 7; 9; 11; 13; 16; 19; 23; 27; 31; 36 *	Glycolysis/gluconeogenesis D, energy reserves D, stress response (general), cell wall, ATP/GTP binding, carbohydrate transport, oxidation reduction, translation regulation	Mitochondria (general, ETC, membrane) M, stress response (osmotic), DNA replication G, intracellular signaling, cytoskeleton, unfolded protein binding P