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Table 1 Groups of relevant biological processes regulated at the protein-expression level

From: Growth control of the eukaryote cell: a systems biology study in yeast

Upregulated   
Biological process Proteins (examples) p-value (GO studies)
Cellular biosynthesis (81) Ser3p, Cpa1p, Lia1p Rpl10p 1.1E-29
Amino-acid and derivative metabolism (33) Gln1p, Leu1p, Lys4p 2.6E-21
Translation (42) Rpl6ap, Mes1p, Sui3p, Fun12p 4.8E-13
Macromolecule biosynthesis (48) Mdh2p, Rpl3p, Mes1p, Ths1p 5.7E-12
tRNA aminoacylation (9) Mes1p, Cdc60p, Ded81p 9.7E-9
Ribosome biogenesis and assembly (22) Nug1p, Rpl30p, Nop58p, Yf3p 3.2E-7
Purine nucleotide metabolism (8) Ade17p, Ade1p, Hpt1p 3.8E-6
Sulfur metabolism (8) Ecm17p, Met10p, Trx2p, Sam2p 2.2E-5
Organic-acid biosynthesis (4) Ald6p, Fas1p, Fas2p 3.6E-4
Regulation of protein metabolism (6) Asc1p, Cap2p, Rpl30p 1.2E-3
rRNA processing (8) Nug1p, Has1p, Utp10p 1.8E-2
Downregulated   
Cellular carbohydrate metabolism (19) Gre2p, Tsl1p, Tps1p, Eno1p 2E-7
Coenzyme metabolism (14) Pan5p, Mdh3p, Npt1p 5.8E-7
Response to stress (27) Pol30p, Hsp104p, Rvs161p 9.8E-7
Response to stimulus (31) Lap3p, Akr1p, Ycf1p, Fet3p 1.1E-5
Cellular macromolecule catabolism (17) Skp1p, Pre3p, Rpn3p, Kar2p 2.3E-4
Vacuole organization and biogenesis (6) Sec17p, Tpm1p, Vtc2p, Vtc3p 3.6E-4
Transport (35) Pet9p, Sar1p, Fet3p, Hxt3p 1.1E-3
Cellular lipid metabolism (11) Ncp1p, Erg1p, Erg27p. Lem3p 7.7E-3
Homeostasis (7) Skp1p, Ahp1p, Vma5p, Zrt3p 2E-2
  1. Groups of relevant biological processes regulated at the protein expression level from growth rates 0.1 to 0.2/h under carbon limitation are shown here. Proteins significantly upregulated or downregulated with increasing growth rate (relative fold-changes greater than 20%, 141 proteins) from iTRAQ studies were analyzed by GO studies (GO tool, SGD Term Finder [42]). Numbers of proteins obtained per biological process are included in brackets. Full lists of results, including genes significantly regulated at the protein expression level, for each biological process are provided in Additional data file 2 (Tables S19 and S20).