Table 2 Classification of transcripts differentially expressed in response to Otx2 and otd overexpression
Functional class | n otd | notd/N (%) | notd/M (%) | n Otx2 | 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 |