Table 2 of Tarnuzzer, Mol Vis 2005; 11:36-49.


Table 2. ECM, protease, and cell adhesion 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 ECM, protease, and cell adhesion 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.

Extracellular matrix

    Mean OD    Mean OS    OD/OS   GenBank                         Gene
    --------   --------   -----   -------   -------------------------------------------------
     6220.50     356.00   17.47   X14420    procollagen 3α1 subunit precursor (COL3A1)
    13514.67    2569.33    5.26   M14219    bone proteoglycan II precursor (PGS2);
                                            decorin (DCN)
    10850.67    2965.67    3.66   X57527    collagen 8α1 subunit (COL8A1)
    15962.50    6250.50    2.55   U86759    netrin-2
     2571.50    1040.00    2.47   X52022    collagen 6α3 subunit (COL6A3)
    17211.00    7263.00    2.37   U32169    collagen 11α2 subunit (COL11A2)
    23245.50   10108.50    2.30   J03040    secreted protein acidic and rich in cysteine
                                            precursor (SPARC)
    25301.00   11708.67    2.16   J04599    bone/cartilage proteoglycan 1 precursor; biglycan
                                            (BGN); PGS1
    19373.00    9072.00    2.14   X78565    tenascin precursor (TN); hexabrachion (HXB);
                                            cytotactin
     7430.33    4196.33    1.77   M24570    collagen 6α2 subunit (COL6A2)
    12518.33    8021.67    1.56   L22548    collagen 18α1 subunit (COL18A1)
    33012.00   21745.67    1.52   X63168    vitronectin precursor (VTN); serum spreading
                                            factor
    42086.33   29193.67    1.44   M55172    aggrecan core protein precursor (AGC1)
     9569.33    7843.33    1.22   X98085    tenascin-R

    Mean    SD     SE    p value   p Bonferroni
    ----   ----   ----   -------   ------------
    3.42   4.18   1.12    <0.01       <0.01

Proteases

    Mean OD    Mean OS    OD/OS   Genbank                         Gene
    --------   --------   -----   -------   -------------------------------------------------
     7286.00    3924.00    1.86   M18082    placental plasminogen activator inhibitor 2
                                            (PAI-2; PLANH2)
     4273.50    2424.00    1.76   J03210    matrix metalloproteinase 2 (MMP2); 72-kDa
                                            gelatinase A
     2720.00    1597.00    1.70   A03911    glia-derived neurite-promoting factor (GDNPF)
    27584.67   21883.67    1.26   L20471    basigin precursor (BSG); collagenase stimulatory
                                            factor
     3254.00    2688.50    1.21   L23808    matrix metalloproteinase 12 (MMP12);
                                            metalloelastase
    33598.00   29008.00    1.16   D50477    matrix metalloproteinase 16 precursor (MMP16);
                                            (MT-MMP3)
    18031.67   16026.00    1.13   L22005    ubiquitin conjugating enzyme E2 32-kDa
                                            complementing protein
    17593.50   16739.00    1.05   X89579    matrix metalloproteinase 17 (MMP17); (MT-MMP4)
     4734.67    4512.00    1.05   J05070    matrix metalloproteinase 9 (MMP9); 92-kDa type IV
                                            collagenase precursor
    26011.00   24846.50    1.05   M15518    tissue-type plasminogen activator precursor
                                            (T-plasminogen activator; TPA)
    34985.67   35226.67    0.99   X03124    tissue inhibitor of metalloproteinases 1 (TIMP1)
    22062.00   25208.00    0.88   U78095    bikunin; hepatocyte growth factor activator
                                            inhibitor 2
     6218.00    7184.50    0.87   U83117    sentrin; ubiquitin-like protein SMT3C
    24341.33   29685.33    0.82   U60519    caspase-10 precursor (CASP10); ICE-LIKE
                                            apoptotic protease 4 (ICE-LAP4)
    16435.00   20622.00    0.80   U20536    caspase-6 precursor (CASP6); cysteine protease
                                            MCH2 isoforms α+β
     2648.50    3352.00    0.79   X57766    matrix metalloproteinase 11 (MMP11);
                                            stromelysin 3
     3771.00    5138.33    0.73   D26512    matrix metalloproteinase 14 precursor (MMP14);
                                            (MT-MMP1)
    22046.33   30961.00    0.71   U56390    caspase-9 precursor (CASP9); ICE-like apoptotic
                                            protease 6 (ICE-LAP6)
     4131.33    7641.33    0.54   J05593    tissue inhibitor of metalloproteinases 2 (TIMP2)
     5614.00   15618.00    0.36   U60520    caspase-8 precursor (CASP8); ICE-like apoptotic
                                            protease 5 (ICE-LAP5)
     3038.50    9407.50    0.32   Y08622    matrix metalloproteinase 18 (MMP18)+MMP19
     2802.00    8871.00    0.32   Z30183    tissue inhibitor of metalloproteinases 3 (TIMP3)
       77.00    4573.50    0.02   X07819    matrix metalloproteinase 7 (MMP7); matrilysin

    Mean    SD     SE    p value   p Bonferroni
    ----   ----   ----   -------   ------------
    0.93   0.46   0.09    0.05         1.00

Adhesion

    Mean OD    Mean OS    OD/OS   GenBank                     Gene
    --------   --------   -----   -------   ----------------------------------------
     5132.00    1253.50    4.09   L34060    cadherin 8 (CDH8)
    19216.00    5746.50    3.34   M59911    integrin α3 (ITGA3); galactoprotein
                                            B3 (GAPB3)
    11195.50    3946.00    2.84   L25851    integrin αE precursor (ITGAE)
    20978.00    9735.50    2.15   X74295    integrin α7B precursor (IGA7B)
    13215.33    6316.33    2.09   X87838    β-catenin (CTNNB)
    20526.00   10365.33    1.98   L12350    thrombospondin 2 precursor (THBS2; TSP2)
    28870.33   17711.67    1.63   M73780    integrin β8 precursor (ITGB8)
    43335.00   29328.00    1.48   L36531    integrin α8 (ITGA8)
    26078.00   18182.50    1.43   D13866    α1 catenin (CTNNA1); cadherin
                                            associated protein
    21832.33   15387.67    1.42   U72661    ninjurin-1
    33197.33   24223.67    1.37   M94151    α-catenin related protein (CAPR); α2
                                            catenin (CTNNA2)
    23904.00   19732.50    1.21   U24497    polycystin precursor; autosomal dominant
                                            polycystic kidney disease protein 1
    14286.50   13199.50    1.08   U53786    envoplakin (EVPL)
    19596.67   18559.00    1.06   M62880    integrin β7 precursor (ITGB7)
    10153.50   14233.00    0.71   X53587    integrin β4 (ITGB4); CD104 antigen

    Mean    SD     SE    p value   p Bonferroni
    ----   ----   ----   -------   ------------
    1.86   0.93   0.24    <0.01       <0.01

Tarnuzzer, Mol Vis 2005; 11:36-49 <http://www.molvis.org/molvis/v11/a4/>
©2005 Molecular Vision <http://www.molvis.org/molvis/>
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