TABLE 1.
Functional categories of differentially expressed transcripts affected in SW620 cells treated with docosahexaenoic acid (DHA) (70 μM) at time points indicated
| SW620 Fold Change |
||||||
|---|---|---|---|---|---|---|
| Gene Symbol | Affymetrix ID | Refseq NCBI ID | Description | 12 h | 24 h | 48 h |
| ER Stress Response | ||||||
| ATF3 | 202672_s_at | NM_001030287 | Activating transcription factor 3 | 3.7 | 4.1 | 3.1 |
| NM_001040619 | ||||||
| NM_001674 | ||||||
| NM_004024 | ||||||
| ATF4 | 200779_at | NM_001675 | Activating transcription factor 4 | 2.1 | 2.0 | 1.6 |
| NM_182810 | ||||||
| ATF6 | 203952_at | NM_007348 | Activating transcription factor 6 | 1.3 | 1.2 | — |
| EIF2S1 | 201142_at | NM_004094 | Eukaryotic translation initiation factor 2-α | NC | NC | NC |
| GADD34 | 37028_at | NM_014330 | Growth arrest and DNA-damage-inducible 34 | 6.3 | 3.9 | — |
| NRF2 | 201146_at | NM_006164 | Nuclear factor E2-related factor | 2.0 | 1.8 | — |
| PERK | 218696_at | NM_004836 | PKR-like ER kinase | 1.4 | 2.0 | — |
| VCP | 208649_s_at | NM_007126 | Valocin containing protein | 1.9 | 1.6 | — |
| XBP1 | 200670_at | NM_001079539 | X-box binding protein 1 | 2.0 | 1.8 | — |
| NM_005080 | ||||||
| Chaperones/Protein Folding/UPR Response | ||||||
| DNAJB1 | 200666_s_at | NM_006145 | DnaJ homolog, subfamily B, member 1 | 8.0 | 4.1 | — |
| HMOX1 | 203665_at | NM_002133 | Heme oxygenase (decycling) 1 | 24.0 | 10.6 | 5.7 |
| HSPA1A/B | 200800_s_at | NM_005345 | Heat shock 70 kDa protein 1A/B | 17.8 | 9.8 | 5.1 |
| NM_005346 | ||||||
| HSPA1B | 202581_at | NM_005346 | Heat shock 70 kDa protein 1B | 9.8 | 6.5 | 3.1 |
| HSP47 | 207714_s_at | NM_001235 | Heat shock protein 47 | 4.4 | 1.8 | — |
| Ubiquitine/Proteasome | ||||||
| PSMD1/RPN2 | 211198_s_at | NM_002807 | Proteasome 26S subunit, non-ATPase, 1 | 2.2 | 2.2 | — |
| SQSTM1 | 213112_s_at | NM_003900 | Sequestosome 1 | 7.7 | 6.7 | 5.0 |
| SQSTM1 | 201471_s_at | NM_003900 | Sequestosome 1 | 6.7 | 7.3 | 3.9 |
| Ca2+ Homeostasis | ||||||
| CAMLG | 203538_at | NM_001745 | Calcium modulating ligand | 1.9 | 1.9 | — |
| CAPN2 | 208683_at | NM_001748 | Calpain 2, large subunit | 1.3 | 1.8 | 1.4 |
| CAPN7 | 203356_at | NM_014296 | Calpain 7 | — | 1.5 | — |
| IP3R1 | 203710_at | NM_002222 | Inositol 1,4,5-triphosphate receptor, type 1 | 1.5 | 2.2 | 1.4 |
| IP3R3 | 201189_s_at | NM_002224 | Inositol 1,4,5-triphosphate receptor, type 3 | — | — | 1.3 |
| Antioxidants/Oxidative Stress | ||||||
| CAT | 201432_at | NM_001752 | Catalase | — | −1.4 | — |
| GCLC | 202922_at | NM_001498 | Glutamate-cysteine ligase, catalytic subunit | 1.6 | 1.3 | — |
| GCLM | 203925_at | NM_002061 | Glutamate-cysteine ligase, modifier subunit | 3.7 | 3.5 | 2.0 |
| HMOX1 | 203665_at | NM_002133 | Heme oxygenase (decycling) 1 | 24.0 | 10.6 | 5.7 |
| SOD1 | 200642_at | NM_000454 | Superoxide dismutase 1 | 1.5 | 1.6 | — |
| TXNRD1 | 201266_at | NM_003330 | Thioredoxin reductase 1 | 3.2 | 2.9 | 1.9 |
| NM_182729 | ||||||
| NM_182742 | ||||||
| NM_182743 | ||||||
| Cell Cycle/Apoptosis | ||||||
| BAG3 | 217911_s_at | NM_004281 | BCL2-associated athanogene 3 | 9.9 | 5.4 | — |
| CASP4 | 209310_s_at | NM_001225 | Caspase 4 | 1.6 | 2.9 | — |
| NM_033306 | ||||||
| NM_033307 | ||||||
| CASP7 | 207181_s_at | NM_001227 | Caspase 7 | 1.6 | 2.1 | — |
| NM_033338 | ||||||
| NM_033339 | ||||||
| NM_033340 | ||||||
| CCND1 | 208712_at | NM_053056 | Cyclin D1 | −1.7 | −2.0 | — |
| TRIB3 | 218145_at | NM_021158 | Tribbles homolog 3 (Drosophila) | 7.4 | 6.5 | 3.3 |
| Cholesterol Biosynthesis, Uptake, Metabolism, and Transport | ||||||
| CAV1 | 203065_s_at | NM_001753 | Caveolin 1, caveolae protein, 22 kDa | −1.5 | −1.4 | — |
| DHCR24 | 200862_at | NM_014762 | 24-dehydrocholesterol reductase | −1.6 | −1.7 | — |
| DHCR7 | 201791_s_at | NM_001360 | 7-dehydrocholesterol reductase | −1.6 | −1.5 | — |
| FDPS | 201275_at | NM_002004 | Farnesyl diphosphate synthase | −1.3 | −1.2 | — |
| HMGCR | 202539_s_at | NM_000859 | 3-hydroxy-3-methylglutaryl-CoA reductase | NC | NC | NC |
| LDLR | 202068_s_at | NM_000527 | Low density lipoprotein receptor | 2.4 | 2.4 | — |
| LSS | 202245_at | NM_002340 | Lanosterol synthase | −1.3 | — | |
| NPC1 | 202679_at | NM_000271 | Niemann-Pick disease, type C1 | 3.0 | 4.5 | 1.9 |
| NPC2 | 200701_at | NM_006432 | Niemann-Pick disease, type C2 | 1.5 | 1.5 | |
| OSBP | 201800_s_at | NM_002556 | Oxysterol binding protein | 1.4 | 1.4 | — |
| PMVK | 203515_s_at | NM_006556 | Phosphomevalonate kinase | -1.3 | −1.8 | — |
| SREBP2 | 201247_at | NM_004599 | Sterol regulatory element binding protein 2 | NC | NC | NC |
| TM7SF2 | 210130_s_at | NM_003273 | Transmembrane 7 superfamily member 2 | −1.4 | −1.9 | — |
| VLDLR | 209822_s_at | NM_001018056 | Very low density lipoprotein receptor | 1.6 | 1.6 | — |
| NM_003383 | ||||||
NC, no change; UPR, unfolded protein response.