Table 4 of
Tarnuzzer, Mol Vis 2005;
11:36-49.Table 4 of
Tarnuzzer, Mol Vis 2005;
11:36-49.
Table 4. Cell cycle, transcription, and apoptosis related genes expressed in aphakic versus normal monkey eyes
Mean adjusted intensities for the three arrays, fold increases and Genbank accession numbers (as noted in Clontech Atlas software) are given for cell cycle, transcription, and apoptosis transcripts expressed in the aphakic eye as determined using AtlasImage software. Mean fold change, standard deviation, standard error of the mean, and p value with and without Bonferroni correction for multiple comparisons are provided for each functional classification. A p value of less than 0.05 was considered statistically significant.
Cell cycle
Mean OD Mean OS OD/OS Genbank Gene
-------- -------- ----- -------- ----------------------------------------------
2176.50 1184.00 1.84 M63618 bullous pemphigoid antigen 1 (BPAG1; BPA);
hemidesmosomal plaque protein
15393.67 12783.67 1.20 L29220 CDC-like kinase 3 (CLK3)
17130.00 3962.50 4.32 U59435 cell cycle protein P38-2G4 homolog; HG4-1
1197.50 1106.50 1.08 X66357 cell division protein kinase 3
3824.33 2850.67 1.34 M14505 cell division protein kinase 4;
cyclin dependent kinase 4 (CDK4); PSK-J3
4742.00 2516.50 1.88 X66364 cell division protein kinase 5 (CDK5); tau
protein kinase II catalytic subunit
21432.00 8629.50 2.48 L25676 cell division protein kinase 9 (CDK9);
serine/threonine protein kinase PITALRE
12650.00 3110.00 4.07 AF016582 checkpoint kinase 1 (CHK1)
3336.00 2483.00 1.34 U68723 checkpoint suppressor 1
7380.00 2501.00 2.95 L27211 cyclin dependent kinase 4 inhibitor
(CDK4I; CDKN2); p16-INK4; multiple tumor
suppressor 1 (MTS1)
43494.00 35400.00 1.23 U40343 cyclin dependent kinase 4 inhibitor D
(CDKN2D); p19-INK4D
8412.00 3859.50 2.18 M68520 cyclin dependent protein kinase 2 (CDK2);
p33 protein kinase
12720.33 13474.67 0.94 U25265 dual specificity mitogen activated protein
kinase kinase 5 (MAP kinase kinase 5; MAPKK 5;
MEK5)
42309.33 20858.33 2.03 L05624 dual specificity mitogen activated protein
kinase kinase 1 (MAP kinase kinase 1; MAPKK 1;
MKK1)
12882.50 3145.00 4.10 U25278 extracellular signal regulated kinase 5
(ERK5); BMK1 kinase
2664.50 888.50 3.00 X79483 extracellular signal regulated kinase 6
(ERK6); stress activated protein kinase-3
10074.33 8135.00 1.24 D13365 growth inhibitory factor; metallothionein-III
(MT-III)
11768.00 3013.50 3.91 L13698 growth arrest specific protein-1 (GAS1)
21256.00 12154.00 1.75 AF005482 histone deaceytlase 3C
10280.00 6620.50 1.55 J05272 IMP dehydrogenase 1
5776.00 3245.50 1.78 AF036906 linker for activation of T-cells (LAT)
5220.00 9412.00 0.55 U78876 MAPK/ERK kinase kinase 3 (MEK kinase 3; MEKK3)
15442.00 12363.00 1.25 AF014118 membrane associated kinase (MYT1)
11987.50 9982.50 1.20 D63878 NEDD5 protein homolog; DIFF6; KIAA0158
11483.67 12235.33 0.94 Y10256 NIK serine/threonine protein kinase
11147.67 5790.00 1.93 L20320 protein serine/threonine kinase STK1; cell
division protein kinase 7 (CDK7)
5364.00 13872.00 0.39 L07597 ribosomal protein S6 kinase II alpha 1
(S6KII-alpha 1); ribosomal S6 kinase 1 (RSK1)
4066.00 1080.50 3.76 U11050 serine/threonine-protein kinase NEK2;
NIMA-related protein kinase 2
17942.00 14740.50 1.22 Z29067 serine/threonine-protein kinase NEK3;
NIMA-related protein kinase 3; HSPK 36
38529.50 29695.00 1.30 U18422 transcription factor DP2 (Humdp2); E2F
dimerization partner 2
4332.00 3580.00 1.21 U15642 transcription factor E2F5
Mean SD SE p value p Bonferroni
---- ---- ---- ------- ------------
1.66 0.61 0.36 <0.01 <0.01
Apoptosis
Mean OD Mean OS OD/OS Genbank Gene
-------- -------- ----- -------- ----------------------------------------------
4838.50 13615.50 0.36 L22474 apoptosis regulator bax
10922.00 19260.00 0.57 L38503 glutathione S-transferase theta 2
24341.33 29685.33 0.82 U60519 caspase-10 precursor (CASP10); ICE-LIKE
apoptotic protease 4 (ICE-LAP4)
5614.00 15574.00 0.36 U60520 caspase-8 precursor (CASP8); ICE-like
apoptotic protease 5 (ICE-LAP5)
22046.33 30961.00 0.71 U56390 caspase-9 precursor (CASP9); ICE-like
apoptotic protease 6 (ICE-LAP6)
16268.00 11026.00 1.48 U69161 CC3 (CC3)
34706.50 29643.50 1.17 U21092 CD40 receptor associated factor 1 (CRAF1)
3399.50 2409.00 1.41 AF016268 death receptor 5 (DR5); cytotoxic TRAIL
receptor 2 (TRICK2A)
3937.50 16276.00 0.24 X76104 death associated protein kinase 1
(DAP kinase 1; DAPK1)
9066.33 14260.33 0.64 U45879 inhibitor of apoptosis protein 2
(HIAP2; IAP2) + IAP homolog B
3572.00 9423.00 0.38 M35663 interferon inducible RNA dependent protein
kinase (P68 kinase)
11483.67 12108.67 0.95 Y10256 NIK serine/threonine protein kinase
6380.67 9283.67 0.69 M84820 retinoic acid receptor beta (RXR-beta; RXRB)
4202.67 11989.67 0.35 X07282 retinoic acid receptor epsilon (RAR-epsilon)
10052.00 18972.00 0.53 AF017986 secreted apoptosis related protein 1 (SARP1)
6218.00 7184.50 0.87 U83117 sentrin; ubiquitin-like protein SMT3C;
ubiquitin-homology domain protein PIC1
26008.67 28770.33 0.90 U04806 SL cytokine precursor; FLT3 ligand (FLT3LG)
15207.67 15039.67 1.01 M32315 tumor necrosis factor receptor 2 (TNFR2)
9526.00 10745.50 0.89 U12595 tumor necrosis factor type 1 receptor
associated protein (TRAP1)
2588.33 4353.33 0.59 Y09392 WSL protein + TRAMP + Apo-3 + death domain
receptor 3 (DDR3)
Mean SD SE p value p Bonferroni
---- ---- ---- ------- ------------
0.75 0.35 0.08 <0.01 <0.01
Transcription
Mean OD Mean OS OD/OS Genbank Gene
-------- -------- ----- -------- ----------------------------------------------
14939.50 16184.50 0.92 S73885 AP4 basic helix-loop-helix DNA binding protein
21020.00 20606.50 1.02 AF006515 CHD3
3336.00 2483.00 1.34 U68723 checkpoint suppressor 1
10489.67 12877.67 0.81 L16785 c-myc purine binding transcription factor puf;
nucleoside diphosphate kinase B
24704.33 27653.33 0.89 X52541 early growth response protein 1 (hEGR1);
transcription factor ETR103
5806.50 4330.00 1.34 M25269 elk-1; ets-related proto-oncogene
2664.00 3835.00 0.69 Z36715 ets domain protein elk-3; NET; SRF accessory
protein 2 (SAP2)
9307.50 6295.00 1.48 X16707 fos-related antigen (FRA1)
21256.00 12154.00 1.75 AF005482 histone deaceytlase 3C
2991.00 4280.33 0.70 D11117 homeobox protein HOX-D3; HOX-4A
13716.00 13455.00 1.02 U91616 IkappaB epsilon (IKBE)
3642.00 4007.00 0.91 X14454 interferon regulatory factor 1 (IRF1)
8328.00 8932.00 0.93 Z56281 interferon regulatory factor 3 (IRF3)
4308.00 6497.50 0.66 L19067 NF-kappaB transcription factor p65
subunit; RELA; NFKB3
6395.67 9283.67 0.69 M84820 retinoic acid receptorβ (RXR-beta; RXRB)
4202.67 11989.67 0.35 X07282 retinoic acid receptorε (RAR-epsilon)
13890.67 15272.33 0.91 M24857 retinoic acid receptorγ1 (RAR-gamma 1; RARG)
1868.00 2399.00 0.78 J03161 serum response factor (SRF)
17948.50 23467.00 0.76 M97935 signal transducer and activator of
transcription 1 alpha/beta (STAT1)
38529.50 29695.00 1.30 U18422 transcription factor DP2 (Humdp2); E2F
dimerization partner 2
4332.00 3580.00 1.21 U15642 transcription factor E2F5
8689.00 15616.00 0.56 J03133 transcription factor Sp1 (TSFP1)
2474.00 2952.00 0.84 D89859 zinc finger 5 protein
Mean SD SE p value p Bonferroni
---- ---- ---- ------- ------------
0.95 0.32 0.07 0.248 1.00
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