Table 2.
Classification of transcripts differentially expressed in response to Otx2 and otd overexpression
| Functional class | notd | notd/N (%) | notd/M (%) | nOtx2 | nOtx2/N (%) | nOtx2/M (%) |
| Function unknown (7,108) | 143 | 2.01 | 49.83 | 311 | 4.38 | 45.60 |
| Enzyme (1,872) | 34 | 1.82 | 11.85 | 88 | 4.70 | 12.90 |
| Transcription factor (940) | 23 | 2.45 | 8.01 | 69 | 7.34 | 10.12 |
| Signal transduction (462) | 17 | 3.68 | 5.92 | 24 | 5.19 | 3.52 |
| DNA binding (306) | 14 | 4.58 | 4.88 | 27 | 8.82 | 3.96 |
| Transporter (498) | 12 | 2.41 | 4.18 | 19 | 3.82 | 2.79 |
| Motor (406) | 11 | 2.71 | 3.83 | 22 | 5.42 | 3.23 |
| Protein kinase (365) | 10 | 2.74 | 3.48 | 25 | 6.85 | 3.67 |
| Ligand binding or carrier (581) | 9 | 1.55 | 3.14 | 28 | 4.82 | 4.11 |
| Endopeptidase (413) | 8 | 1.94 | 2.79 | 25 | 6.05 | 3.67 |
| Nucleic acid binding (369) | 8 | 2.17 | 2.79 | 21 | 5.69 | 3.08 |
| Cell adhesion (328) | 8 | 2.44 | 2.79 | 15 | 4.57 | 2.20 |
| Structural protein (335) | 7 | 2.09 | 2.44 | 18 | 5.37 | 2.64 |
| Actin binding (157) | 6 | 3.82 | 2.09 | 10 | 6.37 | 1.47 |
| RNA binding (292) | 4 | 1.37 | 1.39 | 13 | 4.45 | 1.91 |
| Transmembrane receptor (251) | 4 | 1.59 | 1.39 | 9 | 3.59 | 1.32 |
| Chaperone (195) | 3 | 1.54 | 1.05 | 14 | 7.18 | 2.05 |
| Cell cycle regulator (190) | 3 | 1.58 | 1.05 | 12 | 6.32 | 1.76 |
| Ion channel (214) | 3 | 1.40 | 1.05 | 7 | 3.27 | 1.03 |
| Protein phosphatase (91) | 3 | 3.30 | 1.05 | 6 | 6.59 | 0.88 |
| DNA repair protein (65) | 3 | 4.62 | 1.05 | 4 | 6.15 | 0.59 |
| Transcription factor binding (64) | 2 | 3.13 | 0.70 | 11 | 17.19 | 1.61 |
| Cytoskeletal structural protein (121) | 2 | 1.65 | 0.70 | 6 | 4.96 | 0.88 |
| DNA replication factor (42) | 2 | 4.76 | 0.70 | 5 | 11.90 | 0.73 |
| Defense/immunity protein (64) | 2 | 3.13 | 0.70 | 4 | 6.25 | 0.59 |
| G-protein linked receptor (103) | 2 | 1.94 | 0.70 | 3 | 2.91 | 0.44 |
| Receptor (97) | 2 | 2.06 | 0.70 | 2 | 2.06 | 0.29 |
| Cytochrome P450 | 2 | 14.29 | 0.70 | 0 | 0 | 0 |
| Storage protein (25) | 1 | 4.00 | 0.35 | 3 | 12.00 | 0.44 |
| Peptidase (97) | 1 | 1.03 | 0.35 | 3 | 3.09 | 0.44 |
| Lysozyme (8) | 1 | 12.50 | 0.35 | 2 | 25.00 | 0.29 |
| Cyclin-dependent protein kinase (11) | 1 | 9.09 | 0.35 | 2 | 18.18 | 0.29 |
| GABA-B receptor (1) | 1 | 100.00 | 0.35 | 1 | 100.00 | 0.15 |
| Enzyme inhibitor (121) | 1 | 0.83 | 0.35 | 1 | 0.83 | 0.15 |
| Ecdysteroid hormone receptor (2) | 1 | 50.00 | 0.35 | 0 | 0 | 0 |
| 3',5'-cyclic-nucleotide phosphodiesterase (1) | 1 | 100.00 | 0.35 | 0 | 0 | 0 |
| FK506 binding (2) | 1 | 50.00 | 0.35 | 0 | 0 | 0 |
| Peptidylprolyl isomerase (3) | 1 | 33.33 | 0.35 | 0 | 0 | 0 |
| Neurotransmitter transporter (29) | 1 | 3.45 | 0.35 | 0 | 0.00 | 0.00 |
| Steroid hormone receptor (16) | 1 | 6.25 | 0.35 | 0 | 0.00 | 0.00 |
| Acid phosphatase (5) | 1 | 20.00 | 0.35 | 0 | 0.00 | 0.00 |
| Arginine-tRNA ligase (2) | 1 | 50.00 | 0.35 | 0 | 0.00 | 0.00 |
| Carboxypeptidase (1) | 1 | 100.00 | 0.35 | 0 | 0.00 | 0.00 |
| Caspase activator(1) | 1 | 100.00 | 0.35 | 0 | 0.00 | 0.00 |
| Protein tyrosine phosphatase (9) | 0 | 0.00 | 0.00 | 4 | 44.44 | 0.59 |
| Protein serine/threonine kinase (43) | 0 | 0.00 | 0.00 | 4 | 9.30 | 0.59 |
| Chromatin binding (16) | 0 | 0.00 | 0.00 | 4 | 25.00 | 0.59 |
| Ubiquitin conjugating enzyme (12) | 0 | 0.00 | 0.00 | 3 | 25.00 | 0.44 |
| Structural protein of ribosome (136) | 0 | 0.00 | 0.00 | 3 | 2.21 | 0.44 |
| Casein kinase I (6) | 0 | 0.00 | 0.00 | 3 | 50.00 | 0.44 |
| Calcium binding (18) | 0 | 0.00 | 0.00 | 3 | 16.67 | 0.44 |
| Ubiquitin (14) | 0 | 0.00 | 0.00 | 2 | 14.29 | 0.29 |
| Translation factor (70) | 0 | 0.00 | 0.00 | 2 | 2.86 | 0.29 |
| Transcription co-repressor (3) | 0 | 0.00 | 0.00 | 2 | 66.67 | 0.29 |
| GTP binding (14) | 0 | 0.00 | 0.00 | 2 | 14.29 | 0.29 |
| Glutathione transferase (7) | 0 | 0.00 | 0.00 | 2 | 28.57 | 0.29 |
| Furin (2) | 0 | 0.00 | 0.00 | 2 | 100.00 | 0.29 |
| Electron transfer (35) | 0 | 0.00 | 0.00 | 2 | 5.71 | 0.29 |
| Ubiquitinyl hydrolase 1 (2) | 0 | 0.00 | 0.00 | 1 | 50.00 | 0.15 |
| Ubiquitin-specific protease (5) | 0 | 0.00 | 0.00 | 1 | 20.00 | 0.15 |
| Ubiquitin-like conjugating enzyme (1) | 0 | 0.00 | 0.00 | 1 | 100.00 | 0.15 |
| Tubulin-tyrosine ligase (7) | 0 | 0.00 | 0.00 | 1 | 14.29 | 0.15 |
| Transmembrane receptor protein tyrosine phosphatase (4) | 0 | 0.00 | 0.00 | 1 | 25.00 | 0.15 |
| Transmembrane receptor protein tyrosine kinase (7) | 0 | 0.00 | 0.00 | 1 | 14.29 | 0.15 |
| Transcription factor, cytoplasmic sequestering (1) | 0 | 0.00 | 0.00 | 1 | 100.00 | 0.15 |
| Transcription co-activator (2) | 0 | 0.00 | 0.00 | 1 | 50.00 | 0.15 |
| Thioredoxin (4) | 0 | 0.00 | 0.00 | 1 | 25.00 | 0.15 |
| Spermidine synthase (1) | 0 | 0.00 | 0.00 | 1 | 100.00 | 0.15 |
| SNF1A/AMP-activated protein kinase (1) | 0 | 0.00 | 0.00 | 1 | 100.00 | 0.15 |
| SH3/SH2 adaptor protein (2) | 0 | 0.00 | 0.00 | 1 | 50.00 | 0.15 |
| Sarcosine oxidase (2) | 0 | 0.00 | 0.00 | 1 | 50.00 | 0.15 |
| Ribulose-phosphate 3-epimerase (1) | 0 | 0.00 | 0.00 | 1 | 100.00 | 0.15 |
| Receptor signaling protein tyrosine phosphatase (1) | 0 | 0.00 | 0.00 | 1 | 100.00 | 0.15 |
| Protein tagging (2) | 0 | 0.00 | 0.00 | 1 | 50.00 | 0.15 |
| Prenylated protein tyrosine phosphatase (1) | 0 | 0.00 | 0.00 | 1 | 100.00 | 0.15 |
| Phosphoserine phosphatase (1) | 0 | 0.00 | 0.00 | 1 | 100.00 | 0.15 |
| Multicatalytic endopeptidase (4) | 0 | 0.00 | 0.00 | 1 | 25.00 | 0.15 |
| mRNA (guanine-N7)-methyltransferase (1) | 0 | 0.00 | 0.00 | 1 | 100.00 | 0.15 |
| Mitochondrial processing peptidase(1) | 0 | 0.00 | 0.00 | 1 | 100.00 | 0.15 |
| MAP kinase kinase (3) | 0 | 0.00 | 0.00 | 1 | 33.33 | 0.15 |
| Inositol-1,4,5-triphosphate receptor (1) | 0 | 0.00 | 0.00 | 1 | 100.00 | 0.15 |
| Electron transfer flavoprotein (1) | 0 | 0.00 | 0.00 | 1 | 100.00 | 0.15 |
| Effector caspase (3) | 0 | 0.00 | 0.00 | 1 | 33.33 | 0.15 |
| DNA-directed RNA polymerase III (7) | 0 | 0.00 | 0.00 | 1 | 14.29 | 0.15 |
| Cyclin (5) | 0 | 0.00 | 0.00 | 1 | 20.00 | 0.15 |
| CDP-diacylglycerol-serine O-phosphatidyltransferase (1) | 0 | 0.00 | 0.00 | 1 | 100.00 | 0.15 |
| Caspase (5) | 0 | 0.00 | 0.00 | 1 | 20.00 | 0.15 |
| cAMP-dependent protein kinase regulator (1) | 0 | 0.00 | 0.00 | 1 | 100.00 | 0.15 |
| cAMP-dependent protein kinase catalyst (3) | 0 | 0.00 | 0.00 | 1 | 33.33 | 0.15 |
| cAMP-dependent protein kinase (1) | 0 | 0.00 | 0.00 | 1 | 100.00 | 0.15 |
| Amine oxidase (flavin-containing) (7) | 0 | 0.00 | 0.00 | 1 | 14.29 | 0.15 |
| 3-oxo-5-alpha-steroid 4-dehydrogenase (1) | 0 | 0.00 | 0.00 | 1 | 100.00 | 0.15 |
Genes that were differentially expressed following ubiquitous overexpression of otd or human Otx2, grouped according to Gene Ontology (GO) functional classes. n, Number of transcripts detected that belong to an individual class. N, Number of transcripts represented on the chip for each functional class; the value of N for each functional class is given in parentheses following the class name. n/N × 100, Percentage of transcripts that were differentially regulated for each functional class relative to the total number of transcripts in that class represented on the chip. M, Total number of differentially expressed transcripts (of all classes) following overexpression of otd or human Otx2 (p ≤ 0.001); for otd and Otx2, M is 287 and 682 respectively. n/M × 100, Percentage of transcripts that were differentially regulated in each functional class relative to the the total number of differentially regulated transcripts for otd and Otx2.