Table 3 of
Tarnuzzer, Mol Vis 2005;
11:36-49.Table 3 of
Tarnuzzer, Mol Vis 2005;
11:36-49.
Table 3. Growth factor, cell receptor, and cytoskeleton 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 growth factor, cell receptor, and cytoskeleton 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.
Growth factors
Mean OD Mean OS OD/OS Genbank Gene
-------- -------- ----- -------- --------------------------------------------------
26040.00 28468.00 0.91 M15530 B-cell growth factor 1 precursor (BCGF1)
5410.33 5191.00 1.04 M22489 bone morphogenetic protein 2A (BMP2A)
7079.33 5965.00 1.19 D30751 bone morphogenetic protein 4 (BMP4)
3314.00 4047.50 0.82 L09753 CD30 ligand (CD30L); CD153 antigen
21218.00 18089.33 1.17 M65199 endothelin 2 (ET2)
8038.00 3108.00 2.59 L19063 glial cell line-derived neurotropic factor
precursor (GDNF)
3820.00 3261.50 1.17 M27968 heparin binding growth factor 2 precursor (HBGF2)
8793.67 6317.33 1.39 M60718 hepatocyte growth factor-like protein
10765.33 10371.33 1.04 M27544 insulin-like growth factor IA precursor (IGF1A)
28232.00 22073.00 1.28 X01992 interferon gamma precursor (IFN-gamma; IFNG);
immune interferon
14728.00 14994.00 0.98 K02770 interleukin-1 beta precursor (IL-1; IL1B);
catabolin
16710.00 18179.50 0.92 M57627 interleukin-10 precursor (IL-10)
34588.00 25170.50 1.37 L06801 interleukin-13 precursor (IL-13); NC30
6542.00 5797.00 1.13 X04688 interleukin-5 precursor (IL-5); T-cell
replacing factor (TRF)
8252.00 13557.00 0.61 X04602 interleukin-6 precursor (IL-6)
17640.00 13879.50 1.27 AF028593 jagged 1 (HJ1)
17984.00 12224.50 1.47 AF003521 jagged2 (JAG2)
7277.33 5545.33 1.31 X04571 kidney epidermal growth factor (EGF); urogastrone
7770.00 3373.50 2.30 M86528 neurotrophin-4 (NT4); NT5 + NT6-alpha +
NT6-beta + NT6-gamma
24693.00 26041.67 0.95 X54936 placenta growth factors 1 + 2 (PLGF1 + PLGF2)
5438.67 6204.67 0.88 X06374 platelet-derived growth factor A subunit
precursor (PDGFA; PDGF1)
1421.67 2565.33 0.55 X02811 platelet-derived growth factor B subunit
precursor (PDGFB; PDGF2)
8375.00 9218.50 0.91 X52946 heparin binding growth associated molecule
(HB-GAM)
21414.00 17763.00 1.21 Y00064 secretogranin I precursor (SGI); chromogranin B
14863.00 12430.33 1.20 U33920 semaphorin
26008.67 28770.33 0.90 U04806 SL cytokine precursor; FLT3 ligand (FLT3LG)
6842.50 5578.50 1.23 U16752 stromal cell derived factor 1 precursor (SDF1)
18377.33 19551.00 0.94 M96955 teratocarcinoma-derived growth factor 1 (TDGF1)
5419.50 1868.00 2.90 M19154 transforming growth factor beta2
precursor (TGF-beta2; TGFB2)
15469.67 17885.33 0.86 X02812 transforming growth factor-beta (TGF-beta; TGFB)
1250.50 3544.00 0.35 J03241 transforming growth factor-beta 3 (TGF-beta3)
20304.00 19347.50 1.05 Z71621 Wnt-13
22016.00 22983.50 0.96 X91940 Wnt-8B
Mean SD SE p value p Bonferroni
---- ---- ---- ------- ------------
1.18 0.52 0.09 0.04 1.00
Cell receptors
Mean OD Mean OS OD/OS Genbank Gene
-------- -------- ----- -------- --------------------------------------------------
17622.50 9664.00 1.82 L06139 angiopioetin 1 receptor; tyrosine-protein kinase
receptor TIE-2
27114.67 18144.33 1.49 X60592 CDW40 antigen; CD40L receptor precursor
12048.67 10117.00 1.19 U33635 colon carcinoma kinase 4 precursor (CCK4)
20767.67 19812.00 1.05 U28811 cysteine-rich fibroblast growth factor receptor
3399.50 2409.00 1.41 AF016268 death receptor 5 (DR5); cytotoxic TRAIL receptor 2
(TRICK2A)
5448.00 2365.50 2.30 L03840 fibroblast growth factor receptor 4 (FGFR4)
4398.00 4864.00 0.90 L03380 gonadotropin-releasing hormone receptor (GNRHR)
3885.00 4584.67 0.85 D28481 histamine H1 receptor (HRH1)
28078.00 23999.50 1.17 U12255 IgG receptor FC large subunit P51 precursor (FCRN)
3076.67 3384.33 0.91 M35480 insulin-like growth factor binding protein 2
(IGFBP2)
18151.50 10190.50 1.78 U05875 interferon-gamma (IFN-gamma) receptor beta subunit
precursor
22478.00 21238.00 1.06 U13628 interleukin-15 receptor alpha subunit precursor
14644.33 9910.00 1.48 X13916 low-density lipoprotein receptor-related protein 1
precursor (LRP)
11252.00 11777.00 0.96 X15265 muscarinic acetylcholine receptor M4 (CHRM4)
2416.67 1932.67 1.25 M73980 neurogenic locus notch protein homolog 1 precursor
(NOTCH1)
38253.00 28343.67 1.35 U95299 notch4; hnotch4
26298.00 21522.50 1.22 U21051 probable G protein-coupled receptor GPR4; GPR19
6383.67 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)
13914.67 18272.33 0.76 M24857 retinoic acid receptor gamma 1 (RAR-gamma 1; RARG)
22718.00 14805.00 1.53 X87852 transmembrane protein sex precursor
15207.67 15039.67 1.01 M32315 tumor necrosis factor receptor 2 (TNFR2)
8929.67 2408.33 3.71 X76132 tumor suppressor protein DCC precursor; colorectal
cancer suppressor
11205.67 7914.67 1.42 D17517 tyrosine-protein kinase receptor tyro3 precursor;
rse; sky; dtk
3136.00 3340.33 0.94 X51602 vascular endothelial growth factor receptor 1
(VEGFR1)
2588.33 4353.33 0.59 Y09392 WSL protein + TRAMP + Apo-3 + death domain receptor
3 (DDR3)
Mean SD SE p value p Bonferroni
---- ---- ---- ------- ------------
1.28 0.65 0.13 0.01 0.24
Cytoskeleton
Mean OD Mean OS OD/OS Genbank Gene
-------- -------- ----- ------- ------------------------------------------
2176.50 1184.00 1.84 M63618 bullous pemphigoid antigen 1 (BPAG1; BPA);
hemidesmosomal plaque protein
15576.67 8034.33 1.94 X78817 rho-GAP hematopoietic protein C1 (RGC1);
KIAA0131
8128.00 2866.50 2.84 M34225 type II cytoskeletal 8 keratin (KRT8);
cytokeratin 8 (K8; CK8)
13920.33 14379.33 0.97 X56134 vimentin (VIM)
37499.00 30341.50 1.24 M98776 type II cytoskeletal 11 keratin (KRT11);
cytokeratin 1 (K1; CK1)
22402.50 12797.00 1.75 X67683 type II cytoskeletal 4 keratin (KRT4);
cytokeratin 4 (K4; CK4)
Mean SD SE p value p Bonferroni
----- ---- ---- ------- ------------
1.762 0.64 0.26 0.01 0.08
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