Table 4.
Differential gene expression between confluent, serum withdrawn cultured and native RPE cells sorted by SAM (FDR 1.5%). Genes are sorted by biological function
| Gene name | GenBank Acc No | Score (d) | Fold change* | Biological function |
| 48 Genes overexpressed by confluent serum withdrawn RPE | ||||
| Lectin, galactoside binding, soluble, 9 (galectin 9) | AA434102 | 4.6899019 | NA† | Cell adhesion |
| Cyclin dependent kinase 4 | AA486312 | 4.0367285 | NA | Cell cycle |
| Pospholipase A2 receptor 1, 180 kDa | R91516 | 3.9299213 | NA | Cell cycle |
| Integrin β1 binding protein 1 | AA456882 | 3.8089025 | NA | Cell-matrix adhesion |
| Integrin, α2 (CD49B, α2 subunit of VLA-2 receptor) | AA463610 | 3.7711619 | NA | Cell-matrix adhesion |
| Actin, β | R44290 | 4.0403841 | NA | Cytoskeleton |
| Caldesmon 1 | AA076063 | 3.7303184 | 1.2 | Cytoskeleton; muscle contraction |
| Oxidase (cytochrome c) assembly 1-like | AA598582 | 3.4692439 | 10.5 | Electron transport |
| Tumour suppressor candidate 3 | N66008 | 5.2150083 | NA | Electron transport |
| Cytochrome c oxidase subunit VIc | AA456931 | 4.3479318 | NA | Electron transport |
| Reproduction 8 | AA465570 | 5.736559 | NA | Fertilisation |
| Sialyltransferase 1 (β galactoside α-2,6-sialyltransferase) | AA598652 | 4.0207485 | NA | Immune response |
| Epstein-Barr virus induced gene 3 | AA425028 | 3.4711393 | NA | Immune response |
| Tumour necrosis factor receptor superfamily, member 5 | H98636 | 3.3610776 | NA | Immune response; apoptosis |
| Fucosyltransferase 4 (α(1,3) fucosyltransferase, myeloid specific) | R28447 | 3.8948373 | NA | Metabolism; carbohydrate metabolism |
| Histidine ammonia-lyase | W86776 | 4.2938508 | NA | Metabolism; histidine catabolism |
| Epoxide hydrolase 2, cytoplasmic | R73525 | 5.1584747 | NA | Metabolism; xenobiotic metabolism |
| Protein phosphatase 1, catalytic subunit, α isoform | AA443982 | 3.7866788 | NA | Metabolism; glycogen metabolism |
| CAZ associated structural protein | R52873 | 3.3870227 | NA | Protein degradation |
| Ubiquitin protein ligase E3C | AA284599 | 4.808889 | NA | Protein degradation |
| Ubiquitin conjugating enzyme E2D 3 (UBC4/5 homologue, yeast) | AA017199 | 4.1638422 | NA | Protein degradation |
| Proteasome regulatory particle subunit p44S10 | AA424807 | 3.8497784 | NA | Protein degradation |
| HECT type E3 ubiquitin ligase | R87212 | 3.2685684 | NA | Protein degradation |
| ATPase, H+ transporting, lysosomal V0 subunit a isoform 1 | AA427472 | 16.602038 | 2.8 | Protein degradation; acidification of organelles |
| Protein-O-mannosyltransferase 1 | R13777 | 3.9364101 | NA | Protein modification |
| Aspartylglucosaminidase | R42153 | 3.4922915 | NA | Protein modification |
| Adaptor related protein complex 3, β 2 subunit | H11692 | 4.1620878 | NA | Protein transport |
| SEC13-like 1 (S. cerevisiae) | AA496784 | 4.1282042 | NA | Protein transport |
| α-2-macroglobulin | H06516 | 3.6385137 | NA | Protein transport |
| RAE1 RNA export 1 homolog (S pombe) | AA504128 | 3.4039961 | NA | RNA transport |
| Protein tyrosine phosphatase, non-receptor type 1 | R06605 | 3.5456862 | NA | Signal transduction |
| Zinc finger protein 593 | AA033532 | 3.3121002 | NA | Transcription regulation |
| Signal transducer and activator of transcription 3 interacting protein 1 | N77731 | 3.2713342 | NA | Transcription regulation |
| Zinc finger protein 161 | AA232647 | 6.8052672 | 1.5 | Transcription regulation; cellular defense |
| Topoisomerase (DNA) II alpha 170 kDa | AA504348 | 45.484875 | 17.4 | Transcription regulation; DNA topology |
| Synaptoporin | H98620 | 4.1875559 | NA | Transport |
| ATP binding cassette, subfamily B (MDR/TAP), member 10 | R83875 | 3.3779001 | NA | Transport |
| EST | H66616 | 5.2260079 | NA | Unknown |
| HIV-1 rev binding protein 2 | W52273 | 4.6580643 | 2.6 | Unknown |
| EST | R73909 | 4.2685967 | NA | Unknown |
| EST | AA411554 | 4.1332 | 1.5 | Unknown |
| EST | R02609 | 3.9193518 | 1.5 | Unknown |
| Cisplatin resistance associated | W77812 | 3.8728312 | NA | Unknown |
| Reticulocalbin 1, EF-hand calcium binding domain | AA457719 | 3.3784786 | NA | Unknown |
| Family with sequence similarity 13, member A1 | N51424 | 3.3669014 | NA | Unknown |
| Transcribed sequence with weak similarity to protein ref:NP_060219.1 (H sapiens) hypothetical protein FLJ20294 (H sapiens) | R51835 | 3.3217265 | 10.3 | Unknown |
| Similar to non-histone chromosomal protein HMG-14 (high mobility group nucleosome binding domain 1) (LOC400452), mRNA | R53889 | 3.315474 | NA | Unknown |
| EST | W19429 | 3.2800179 | NA | Unknown |
| 5 genes underexpressed by confluent serum withdrawn RPE | ||||
| Phosphofructokinase, platelet | R38433 | −5.491407 | −2.0 | Metabolism; glycolysis |
| Mannosyl (α-1,6-)-glycoprotein β-1,2-N-acetylglucosaminyltransferase | AA485653 | −3.719321 | −2.0 | Metabolism; oligosaccaride synthesis |
| START domain containing 4, sterol regulated | H11369 | −3.790357 | −2.6 | Metabolism; cholesterol transporter |
| Snail homologue 2 (Drosophila) | H57309 | −3.733474 | −6.3 | Transcription regulation |
| CDNA FLJ42496 fis, clone BRACE2035003 | AA410207 | −4.944185 | −12.2 | Unknown |
*Confluent, serum withdrawn/native RPE; †NA, undetectable in native RPE.