TABLE 1.

Major functional classes of genes affected by rapamycina

Class and subclass (n)ExamplebUnigene no.
Amino acid metabolism (24)
    Catabolism (8 up, 5 down)BCKAD E1 alpha (up)Hs.78950
    tRNA synthetase (7 down)Threonyl-tRNA synthetase (down)Hs.84131
    Amino acid transport (3 down)Neutral amino acid transporter (down)Hs.183556
    Amino acid biosynthesis (1 down)Asparagine synthetase (down)Hs.75692
Lipid metabolism (7)
    Catabolism (2 up)VLACD (up)Hs.82208
    Biosynthesis (5 down)Fatty acid synthase (down)Hs.83190
Nucleotide metabolism (7)
    Salvage pathway (4 up)Adenine deaminase (2) (up)Hs.1217
    De novo biosynthesis (3 down)Uridine monophosphate kinase (down)Hs.75939
Glycolysis (6)Phosphoglycerate mutase (down)Hs.181013
Mitochondria (36)
    Transport (2 up)Adenine nucleotide translocator (2) (up)Hs.164280
    Tricarboxylic acid cycle (1 up, 3 down)Isocitrate dehydrogenase (NADP+) (up)Hs.5337
    Electron transfer chain (2 up, 8 down)NADH-ubiquinone oxidoreductase (down)Hs.75227
    Mitochondrial biogenesis (7 down)Ribosomal protein S12 (2) (down)Hs.9964
Protein synthesis (11)eIF2 alpha (down)Hs.81613
Protein turnover (18)
    Ubiquitin-conjugating enzyme (1 up, 3 down)UBC E2 variant 1 (up)Hs.75875
    Proteasome subunits (7 down)Alpha subunit 3 of proteasome (down)Hs.167106
Stress response (25)
    Heat shock/chaperonin (17 down)Hsp70 (down)Hs.90093
    DNA damage (4 up, 1 down)ERCC 1 (up)Hs.59544
Immune modulator (29)
    Cytokine receptor (3 up)IL-4 receptor (up)Hs.75545
    Surface antigen (8 up)CD53 (up)Hs.82212
Chromatin related (19)
    Histone (9 up)H3 histone, 3A (up)Hs.181307
    Topoisomerase (3 up)DNA topoisomerase II alpha (up)Hs.156346
Transcription factors (33)c-Myc (3) (up)Hs.79070
Cell cycle (10)Cdc25A (down)Hs.1634
  • a There are 504 genes affected by rapamycin at 12 and 24 h, of which 114 are of unknown function. All 390 known genes were functionally annotated by searching the Unigene and PubMed databases. up, up-regulated; down, down-regulated.

  • b Numbers in parentheses indicate that rapamycin affected more than one entry representing the same gene on the U95 Av2 chips.