TABLE 1.
Major functional classes of genes affected by rapamycina
| Class and subclass (n) | Exampleb | Unigene 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.