Table 2 of Wride, Mol Vis 2003; 9:360-396.


Table 2. Onto-ExpressTM analysis of the 1,668 genes expressed at above background plus 2 SD levels in at least one of the lens samples

Results of Onto-ExpressTM analysis of the 1,668 genes expressed at above background plus 2 SD levels in at least one of the lens samples to determine the biological processes in which they are involved according to Gene OntologyTM. The genes are listed in their categories in descending order of number of genes per category. P values are calculated by Onto-ExpressTM by comparing the proportion of genes in a given category identified using the microarray with the total complement of genes in that category on the array. Thereby, groups of genes with smaller p values are represented in the microarray data in greater numbers than would be expected (transcription factors p=0.047; G-Protein Coupled Receptor Signaling Pathway p=0.014). Categories with p<0.05 are labeled with an asterisk ("*"). Genes may appear in more than one category if they have more than one GeneOntologyTM term associated with them.

    Biological      Cluster   Locus    Accession
     process          ID        ID     number(s)                          Gene name                          p value
-----------------   -------   ------   ---------   -------------------------------------------------------   -------
transcription regulation*
                    4316      11863    AI451564    aryl hydrocarbon receptor nuclear translocator             0.047
                    9524      17684    AI430768    Cbp/p300-interacting transactivator, with Glu/Asp-rich
                                                   carboxy-terminal domain, 2
                    7549      13198    AI323295    DNA-damage inducible transcript 3
                    4303      14056    AI323840    enhancer of zeste homolog 2 (Drosophila)
                    28619     23894    AI327310    general transcription factor II H, polypeptide 2 (44
                                                   kDa subunit)
                    29630     14887    AI429623    general transcription factor III C 1
                    22216     14605    AI326808    glucocorticoid-induced leucine zipper
                    215       15414    AI385768    homeo box B6
                    26544     15438    AI385671    homeo box D9
                    7320      17127    AI324173    MAD homolog 3 (Drosophila)
                    100399    17128    AI427147    MAD homolog 4 (Drosophila)
                    10563     17765    AI448197    metal response element binding transcription factor 2
                    101277    29861    AI430751    neuronal d4 domain family member
                    6549      17937    AI385556    Ngfi-A binding protein 2
                    4918      14815    AI447752    nuclear receptor subfamily 3, group C, member 1
                    3507      18227    AI429298    nuclear receptor subfamily 4, group A, member 2
                    27220     18046    AI448923    nuclear transcription factor-Y gamma
                    10723     18628    AI428816    period homolog 3 (Drosophila)
                    304       19645    AI323835    retinoblastoma 1
                    28027     19651    AI323872    retinoblastoma-like 2
                    4081      12394    AI451932    runt related transcription factor 1
                    8249      20846    AI449540    signal transducer and activator of transcription 1
                    21642     20728    AI451311    Spi-C transcription factor (Spi-1/PU.1 related)
                    4605      21385    AI448932    T-box 2
                    103636    21388    AI464523    T-box 5
                    3406      21423    AI324257    transcription factor E2a
                    15755     20466    AI426974    transcriptional regulator, SIN3A (yeast)
                    2137      20467    AI327204    transcriptional regulator, SIN3B (yeast)
                    15781     22282    AI893650    upstream transcription factor 2
                    28230     17134    AI428545    v-maf musculoaponeurotic fibrosarcoma oncogene family,
                                                   protein G (avian)
                    3868      22632    AI447233    YY1 transcription factor
protein amino acid phosphorylation
                    29133     12236    AI465548    budding uninhibited by benzimidazoles 1 homolog, beta      0.286
                                                   (S. cerevisiae)
                    30199     27373    AI449651    casein kinase 1, epsilon
                    18268     12748    AI661472    CDC-like kinase 2
                    118       12566    AI323666    cyclin-dependent kinase 2
                    8534      13649    AI427644    epidermal growth factor receptor
                    25120     26559    AI426929    hormonally upregulated Neu-associated kinase
                    16009     16428    AI528630    IL2-inducible T-cell kinase
                    142       16818    AI573454    lymphocyte protein tyrosine kinase
                    27970     26415    AI894223    mitogen activated protein kinase 13
                    3968      26409    AI427174    mitogen activated protein kinase kinase kinase 7
                    4936      26414    AI385708    mitogen-activated protein kinase 10
                    4597      18555    AI327059    PCTAIRE-motif protein kinase 1
                    28130     18557    AI323675    PCTAIRE-motif protein kinase 3
                    32033     20112    AI448582    ribosomal protein S6 kinase, 90 kD, polypeptide 2
                    22845     20779    AI413783    Rous sarcoma oncogene
                    10154     21754    AI449716    testis specific protein kinase 1
                    34216     22241    AI414377    Unc-51 like kinase 1 (C. elegans)
                    8108      22390    AI465227    wee 1 homolog (S. pombe)
cell growth and/or maintenance
                    7883      11789    AI451571    adenomatosis polyposis coli                                0.217
                    8534      13649    AI427644    epidermal growth factor receptor
                    1424      14042    AI385657    exostoses (multiple) 1
                    20964     14681    AI661491    guanine nucleotide binding protein, alpha o
                    3510      16326    AI452079    inhibin beta E
                    142       16818    AI573454    lymphocyte protein tyrosine kinase
                    880       16341    AI323816    mammary tumor integration site 6
                    734       18176    AI414879    neuroblastoma ras oncogene
                    757       11848    AI324087    ras homolog A2
                    304       19645    AI323835    retinoblastoma 1
                    28027     19651    AI323872    retinoblastoma-like 2
                    22845     20779    AI413783    Rous sarcoma oncogene
                    22670     17246    AI448103    transformed mouse 3T3 cell double minute 2
                    30435     22084    AI450392    tuberous sclerosis 2
                    28230     17134    AI428545    v-maf musculoaponeurotic fibrosarcoma oncogene family,
                                                   protein G (avian)
cell adhesion
                    27291     53414    AI326786    Bystin-like                                                0.274
                    4911      12805    AI425965    Contactin 1
                    4851      13805    AI414256    Endoglin
                    1346      16401    AI450152    Integrin alpha 4
                    27448     18186    AI323974    Neuropilin
                    46724     58998    AI428160    Poliovirus receptor-related 3
                    738       12826    AI528741    Procollagen, type IV, alpha 1
                    22173     20345    AI661333    Selectin, platelet (p-selectin) ligand
                    980       21923    AI327207    Tenascin C
                    14455     21810    AI661287    Transforming growth factor, beta induced, 68 kDa
                    18994     56321    AI426755    Traube
                    3758      12927    AI426143    V-crk-associated tyrosine kinase substrate
metabolism
                    80501     11982    AI327378    ATPase, class V, type 10A                                  0.058
                    14926     11977    AI449437    ATPase, Cu++ transporting, alpha polypeptide
                    25848     12039    AI323918    Branched chain ketoacid dehydrogenase E1, alpha
                                                   polypeptide
                    26940     12408    AI323923    Carbonyl reductase 1
                    10172     13017    AI326235    C-terminal binding protein 2
                    19987     13190    AI325230    Dopachrome tautomerase
                    2820      14635    AI894127    Galactokinase
                    29751     56454    AI324071    Pyrroline-5-carboxylate synthetase (glutamate
                                                   gamma-semialdehyde synthetase)
                    28393     20751    AI894147    Sepiapterin reductase
                    6611      26458    AI326155    Solute carrier family 27 (fatty acid transporter),
                                                   member 2
                    5129      20905    AI430879    Steroid sulfatase
transport
                    15691     11307    AI323653    ATP-binding cassette, sub-family G (WHITE), member 1       0.257
                    29133     12236    AI465548    Budding uninhibited by benzimidazoles 1 homolog, beta
                                                   (S. cerevisiae)
                    3049      54124    AI326913    CDC28 protein kinase 1
                    7417      12445    AI323871    Cyclin D3
                    118       12566    AI323666    Cyclin-dependent kinase 2
                    168789    12577    AI428384    Cyclin-dependent kinase inhibitor 1C (P57)
                    3292      14810    AI385669    Glutamate receptor, ionotropic, NMDA1 (zeta 1)
                    31625     17339    AI323353    Major intrinsic protein of eye lens fiber
                    27970     26415    AI894223    Mitogen activated protein kinase 13
                    12145     19646    AI324260    Retinoblastoma binding protein 4
                    28027     19651    AI323872    Retinoblastoma-like 2
apoptosis
                    692       11800    AI661160    apoptosis inhibitor 5                                      0.169
                    17493     12905    AI426523    CASP2 and RIPK1 domain containing adaptor with death
                                                   domain
                    28814     12368    AI326797    caspase 6
                    10026     14311    AI323465    fat specific gene 27
                    22216     14605    AI326808    glucocorticoid-induced leucine zipper
                    1715      16994    AI327398    lymphotoxin B
                    143798    58801    AI449135    phorbol-12-myristate-13-acetate-induced protein 1
                    544       18611    AI323543    phosphoprotein enriched in astrocytes 15
                    32801     70527    AI662639    Stam binding protein
                    29351     21842    AI425932    TGF-beta1-induced anti-apoptotic factor 1
cell cycle
                    2450      19659    AI893623    Retinol binding protein 1, cellular                        0.28
                    2605      19662    AI326915    Retinol binding protein 4, plasma
                    157511    20516    AI415416    Solute carrier family 20, member 2
                    17322     20518    AI428862    Solute carrier family 22 (organic cation transporter),
                                                   member 2
                    29510     59023    AI413193    Solute carrier family 28 (sodium-coupled nucleoside
                                                   transporter), member 2
                    18300     20532    AI451127    Solute carrier family 3, member 1
                    2446      20983    AI323609    Synaptotagmin 4
                    15755     20466    AI426974    Transcriptional regulator, SIN3A (yeast)
                    2137      20467    AI327204    Transcriptional regulator, SIN3B (yeast)
                    2108      22139    AI323822    Transthyretin
signal transduction
                    4316      11863    AI451564    aryl hydrocarbon receptor nuclear translocator             0.263
                    17493     12905    AI426523    CASP2 and RIPK1 domain containing adaptor with death
                                                   domain
                    12895     20299    AI449147    chemokine (C-C motif) ligand 22
                    32472     14169    AI451464    fibroblast growth factor 14
                    6577      53612    AI448040    PCTAIRE-motif protein kinase 3
                    10723     18628    AI428816    period homolog 3 (Drosophila)
                    23978     23970    AI662563    protein kinase C and casein kinase substrate in
                                                   neurons2
                    20945     67903    AI429553    regulator of G-protein signaling 19 interacting
                                                   protein1
                    8249      20846    AI449540    signal transducer and activator of transcription 1
protein biosynthesis
                    2050      66480    AI465224    eukaryotic translation initiation factor 3, subunit 6      0.35
                    22147     56055    AI450198    GTP binding protein 2
                    70127     19897    AI323900    hypothetical pseudogene ribosomal protein L12
                    880       16341    AI323816    mammary tumor integration site 6
                    142380    26451    AI415314    ribosomal protein L27a
                    11376     54217    AI464570    ribosomal protein L36
                    5291      20103    AI464376    ribosomal protein S5
                    140568    68436    AI894275    RIKEN cDNA 1100001I22 gene
                    27419     69606    AI450131    RIKEN cDNA 2310020P08 gene
G-protein coupled receptor protein signaling pathway*
                    153916    11540    AI465291    adenosine A2a receptor                                     0.014
                    12948     14065    AI413964    coagulation factor II (thrombin) receptor-like 3
                    32191     54393    AI449538    gamma-aminobutyric acid (GABA-B) receptor, 1
                    989       14672    AI528620    guanine nucleotide binding protein, alpha 11
                    202311    14674    AI426467    guanine nucleotide binding protein, alpha 13
                    20964     14681    AI661491    guanine nucleotide binding protein, alpha o
                    30141     14693    AI448892    guanine nucleotide binding protein, beta 2
                    4463      22355    AI385741    vasoactive intestinal peptide receptor 2
cell cycle control
                    7417      12445    AI323871    cyclin D3                                                  0.431
                    8534      13649    AI427644    epidermal growth factor receptor
                    734       18176    AI414879    neuroblastoma ras oncogene
                    2675      18590    AI385687    platelet derived growth factor, alpha
                    22845     20779    AI413783    Rous sarcoma oncogene
                    18213     21808    AI323791    transforming growth factor, beta 2
                    31540     22339    AI450411    vascular endothelial growth factor A
                    28230     17134    AI428545    v-maf musculoaponeurotic fibrosarcoma oncogene family,
                                                   protein G (avian)
intracellular signaling cascade
                    16009     16428    AI528630    IL2-inducible T-cell kinase                                0.142
                    1781      16822    AI451618    lymphocyte cytosolic protein 2
                    142       16818    AI573454    lymphocyte protein tyrosine kinase
                    544       18611    AI323543    phosphoprotein enriched in astrocytes 15
                    22845     20779    AI413783    Rous sarcoma oncogene
                    8249      20846    AI449540    signal transducer and activator of transcription 1
                    33824     76561    AI450660    sorting nexin 7
intracellular protein traffic
                    6836      11840    AI324265    ADP-ribosylation factor 1                                  0.102
                    196526    11845    AI449299    ADP-ribosylation factor 6
                    16710     16211    AI323858    karyopherin (importin) beta 1
                    28375     53421    AI327023    SEC61, alpha subunit (S. cerevisiae)
                    33824     76561    AI450660    sorting nexin 7
                    27393     21855    AI429549    translocator of inner mitochondrial membrane b
electron transport
                    43415     12861    AI893442    cytochrome c oxidase, subunit VI a, polypeptide 1          0.234
                    14022     12868    AI326932    cytochrome c oxidase, subunit VIIIa
                    14781     13086    AI893559    cytochrome P450, family 2, subfamily a, polypeptide 4
                    21758     13106    AI323829    cytochrome P450, family 2, subfamily e, polypeptide 1
                    20115     13142    AI447515    D-amino acid oxidase
                    3533      56551    AI325495    thioredoxin 2                                              0.343
defense response
                    6417      12484    AI323855    CD24a antigen
                    22564     14969    AI447932    histocompatibility 2, class II antigen E beta
                    7043      16149    AI451110    Ia-associated invariant chain
                    41980     17086    AI450786    natural cytotoxicity triggering receptor 1
                    33874     142980   AI450647    toll-like receptor 3
                    154045    56753    AI426251    tumor-associated calcium signal transducer 2
heat shock response*
                    21549     80888    AI326838    Cryac Crystallin, alpha C                                  0.035
                    2982      81489    AI465465    Dnajb1 DnaJ (Hsp40) homolog, subfamily B, member 1
                    197601    15528    AI327085    Hspe1 Heat shock 10 kDa protein 1 (chaperonin 10)
                    22708     12406    AI326777    Serpinh1 Serine (or cysteine) proteinase inhibitor,
                                                   clade H (heat shock protein 47), member 1
histogenesis and organogenesis
                    10663     17172    AI415258    achaete-scute complex homolog-like 1 (Drosophila)          0.49
                    27757     12153    AI327151    bone morphogenetic protein 1
                    215       15414    AI385768    homeo box B6
                    26544     15438    AI385671    homeo box D9
immune response
                    12895     20299    AI449147    chemokine (C-C motif) ligand 22                            0.317
                    22564     14969    AI447932    histocompatibility 2, class II antigen E beta
                    18530     15950    AI661257    interferon activated gene 203
                                       AI451137
                    1715      16994    AI327398    lymphotoxin B
post-translational membrane targeting
                    6417      12484    AI323855    CD24a antigen                                              0.219
                    4911      12805    AI425965    contactin 1
                    1098      53872    AI323833    GPI-anchored membrane protein 1
                    1514      16956    AI326787    lipoprotein lipase
sensory organ development*
                    22830     12957    AI325927    Cryba1 Crystallin, beta A1                                 0.035
                    86656     12958    AI324706    Cryba2 Crystallin, beta A2
                    30374     12966    AI323924    Crygc Crystallin, gamma C
                    20176     12964    AI323909    Mus musculus crystallin, gamma A (Cryga), mRNA
small GTPase mediated signal transduction
                    196526    11845    AI449299    ADP-ribosylation factor 6                                  0.422
                    24443     14569    AI528719    guanosine diphosphate (GDP) dissociation inhibitor 3
                    734       18176    AI414879    neuroblastoma ras oncogene
                    757       11848    AI324087    ras homolog gene family, member A
ubiquitin-dependent protein degradation
                    30097     26440    AI325451    proteasome (prosome, macropain) subunit, alpha type 1      0.445
                    368       19172    AI415623    proteasome (prosome, macropain) subunit, beta type 4
                    9002      22215    AI661496    ubiquitin protein ligase E3A
                    29352     22213    AI413443    ubiquitin-conjugating enzyme E2G 2
cation transport
                    80501     11982    AI327378    ATPase, Class V, type 10A                                  0.475
                    14926     11977    AI449437    ATPase, Cu++ transporting, alpha polypeptide
                    23020     16530    AI414909    potassium channel, subfamily K, member 7
cell cycle arrest
                    168789    12577    AI428384    cyclin-dependent kinase inhibitor 1C (P57)                 0.167
                    7549      13198    AI323295    DNA-damage inducible transcript 3
                    3350      11426    AI449659    microtubule-actin crosslinking factor 1
DNA replication
                    29361     50793    AI427116    origin recognition complex, subunit 3-like (S.             0.422
                                                   cerevisiae)
                    9199      18974    AI451438    polymerase (DNA directed), epsilon 2 (p59 subunit)
                    12145     19646    AI324260    retinoblastoma binding protein 4
embryogenesis and morphogenesis
                    27757     12153    AI327151    bone morphogenetic protein 1                               0.317
                    7320      17127    AI324173    MAD homolog 3 (Drosophila)
                    100399    17128    AI427147    MAD homolog 4 (Drosophila)
mitosis
                    29133     12236    AI465548    budding uninhibited by benzimidazoles 1 homolog, beta      0.239
                                                   (S. cerevisiae)
                    118       12566    AI323666    cyclin-dependent kinase 2
                    8108      22390    AI465227    wee 1 homolog (S. pombe)
proteolysis and peptidolysis*
                    27757     12153    AI327151    bone morphogenetic protein 1                               0.018
                    28814     12368    AI326797    caspase 6
                    21306     17391    AI426335    matrix metalloproteinase 24
ribosome biogenesis
                    70127     19897    AI323900    hypothetical pseudogene ribosomal protein L12              0.056
                    5291      20103    AI464376    ribosomal protein S5
                    32033     20112    AI448582    ribosomal protein S6 kinase, polypeptide 2
synaptic transmission
                    32191     54393    AI449538    gamma-aminobutyric acid (GABA-B) receptor, 1               0.167
                    3292      14810    AI385669    glutamate receptor, ionotropic, NMDA1 (zeta 1)
                    23020     16530    AI414909    potassium channel, subfamily K, member 7
transcription regulation, from Pol II promoter
                    29275     56787    AI415295    achaete-scute complex homolog-like 3 (Drosophila)          0.105
                    3909      20585    AI327369    SWI/SNF related, matrix associated, actin dependent
                                                   regulator of chromatin, subfamily a, member 3
                    15781     22282    AI893650    upstream transcription factor 2
anti-apoptosis
                    692       11800    AI661160    apoptosis inhibitor 5                                      0.263
                    22216     14605    AI326808    glucocorticoid-induced leucine zipper
carbohydrate metabolism
                    2040      12091    AI528555    galactosidase, beta 1                                      0.38
                    103675    50720    AI451106    ribonucleotide reductase M2
cell-matrix adhesion
                    1346      16401    AI450152    integrin alpha 4                                           0.171
                    757       11848    AI324087    ras homolog gene family, member A
common-partner SMAD protein phosphorylation
                    7320      17127    AI324173    MAD homolog 3 (Drosophila)                                 0.093
                    100399    17128    AI427147    MAD homolog 4 (Drosophila)
cytoskeleton organization and biogenesis
                    1000      17901    AI324023    myosin light chain, alkali, fast skeletal muscle           0.453
                    4010      22349    AI414231    villin
DNA repair
                    28619     23894    AI327310    general transcription factor II H, polypeptide 2           0.453
                    12145     19646    AI324260    retinoblastoma binding protein 4
glycolysis
                    7729      11676    AI327146    aldolase 3, C isoform                                      0.171
                    29994     13808    AI325234    enolase 3, beta muscle
hydrogen transport
                    20869     11975    AI451534    ATPase, H+ transporting lysosomal V0 subunit a isoform1    0.093
                    30155     11984    AI385732    ATPase, H+ transporting, V0 subunit C
induction of apoptosis
                    28814     12368    AI326797    caspase 6                                                  0.171
                    143798    58801    AI449135    phorbol-12-myristate-13-acetate-induced protein 1
integrin-mediated signaling pathway
                    1346      16401    AI450152    integrin alpha 4                                           0.359
                    757       11848    AI324087    ras homolog gene family, member A
mRNA splicing
                    6787      20383    AI528616    splicing factor, arginine/serine-rich 3 (SRp20)            0.105
                    28150     81898    AI666563    splicing factor 3b, subunit 1
microtubule-based movement
                    29317     56444    AI326428    ARP10 actin-related protein 10 homolog (S. cerevisiae)     0.359
                    19726     13411    AI326265    dynein, axonemal, heavy chain 11
microtubule-based process
                    86654     17760    AI448037    microtubule-associated protein 6                           0.077
                    1948      21648    AI465254    t-complex testis expressed 1
neurogenesis
                    10663     17172    AI415258    achaete-scute complex homolog-like 1 (Drosophila)          0.252
                    3507      18227    AI429298    nuclear receptor subfamily 4, group A, member 2
protein folding
                    28480     30795    AI427165    FK506 binding protein 3                                    0.38
                    197601    15528    AI327085    heat shock protein 1 (chaperonin 10)
pattern specification
                    215       15414    AI385768    homeo box B6                                               0.093
                    26544     15438    AI385671    homeo box D9
potassium transport
                    424       11933    AI450702    ATPase, Na+/K+ transporting, beta 3 polypeptide            0.459
                    23020     16530    AI414909    potassium channel, subfamily K, member 7
protein kinase cascade*
                    202311    14674    AI426467    guanine nucleotide binding protein, alpha 13               0.035
                    29857     64011    AI326818    neurogranin
protein modification
                    20874     18602    AI666339    peptidyl arginine deiminase, type IV                       0.359
                    9002      22215    AI661496    ubiquitin protein ligase E3A
RHO protein signal transduction
                    202311    14674    AI426467    guanine nucleotide binding protein, alpha 13               0.093
                    757       11848    AI324087    ras homolog gene family, member A
RNA processing
                    16767     53379    AI449004    heterogeneous nuclear ribonucleoprotein A2/B1              0.263
                    111       18521    AI893657    poly(rC) binding protein 2
actin cytoskeleton organization and biogenesis
                    3529      12343    AI528740    capping protein (actin filament) muscle Z-line, alpha 2    0.288
action potential regulation
                    989       14672    AI528620    guanine nucleotide binding protein, alpha 11               0.05
amino acid biosynthesis*
                    29751     56454    AI324071    pyrroline-5-carboxylate synthetase (glutamate              0.035
                                                   gamma-semialdehyde synthetase)
angiogenesis
                    202311    14674    AI426467    guanine nucleotide binding protein, alpha 13               0.05
anion transport
                    569       22334    AI430965    voltage-dependent anion channel 2                          0.05
ATP biosynthesis
                    30155     11984    AI385732    ATPase, H+ transporting, V0 subunit C                      0.288
base conversion/substitution editing
                    153899    56417    AI449308    adenosine deaminase, RNA-specific                          0.05
biosynthesis
                    27419     69606    AI450131    RIKEN cDNA 2310020P08 gene                                 0.288
cell communication
                    26859     14622    AI323309    gap junction membrane channel protein beta 5               0.159
cell differentiation
                    202311    14674    AI426467    guanine nucleotide binding protein, alpha 13               0.159
cell growth
                    18213     21808    AI323791    transforming growth factor, beta 2                         0.05
cell proliferation
                    4078      17345    AI428398    antigen identified by monoclonal antibody Ki 67            0.47
cell shape control
                    202311    14674    AI426467    guanine nucleotide binding protein, alpha 13               0.159
cell-cell signaling
                    26859     14622    AI323309    gap junction membrane channel protein beta 5               0.288
cellular defense response
                    30557     21473    AI449302    T-cell receptor alpha chain                                0.288
central nervous system development
                    9524      17684    AI430768    Cbp/p300-interacting transactivator, with Glu/Asp-rich     0.05
                                                    carboxy-terminal domain, 2
chemotaxis
                    12895     20299    AI449147    chemokine (C-C motif) ligand 22                            0.47
cholesterol metabolism
                    28099     20652    AI385523    sterol O-acyltransferase 1                                 0.05
chromatin assembly/disassembly
                    28003     12419    AI893653    chromobox homolog 5 (Drosophila HP1a)                      0.288
chromatin modeling
                    29546     56456    AI447773    BRG1/brm-associated factor 53A                             0.05
chromosome organization and biogenesis (sensu Eukarya)
                    193557    15269    AI323498    similar to germinal histone H4 gene                        0.47
copper ion transport
                    14926     11977    AI449437    ATPase, Cu++ transporting, alpha polypeptide               0.05
cytokine and chemokine mediated signaling pathway
                    103809    58184    AI414253    rcd1 (required for cell differentiation) homolog 1         0.159
                                                   (S. pombe)
detoxification response
                    4316      11863    AI451564    aryl hydrocarbon receptor nuclear translocator             0.05
developmental processes
                    4524      16825    AI465231    LIM domain binding 1                                       0.224
DNA dependent DNA replication
                    214703    117599   AI451189    helicase (DNA) B                                           0.05
DNA methylation
                    322       17191    AI449099    methyl-CpG binding domain protein 2                        0.288
DNA modification
                    20915     21976    AI428343    topoisomerase (DNA) III beta                               0.05
DNA packaging
                    2756      15312    AI426113    similar to nonhistone chromosomal protein HMG-14 -         0.415
                                                   mouse
DNA replication, priming
                    214703    117599   AI451189    helicase (DNA) B                                           0.159
DNA topological change
                    20915     21976    AI428343    topoisomerase (DNA) III beta                               0.05
DNA unwinding
                    20915     21976    AI428343    topoisomerase (DNA) III beta                               0.05
dopamine receptor signaling pathway
                    20964     14681    AI661491    guanine nucleotide binding protein, alpha o                0.05
endoderm development
                    1424      14042    AI385657    exostoses (multiple) 1                                     0.05
fatty acid metabolism
                    6611      26458    AI326155    solute carrier family 27 (fatty acid transporter),         0.47
                                                   member 2
galactose metabolism
                    2820      14635    AI894127    galactokinase 1                                            0.05
gastrulation
                    1424      14042    AI385657    exostoses (multiple) 1                                     0.05
glutamate signaling pathway
                    989       14672    AI528620    guanine nucleotide binding protein, alpha 11               0.05
glutathione biosynthesis
                    4559      14598    AI323672    gamma-glutamyltransferase 1                                0.05
glutathione metabolism
                    4559      14598    AI323672    gamma-glutamyltransferase 1                                0.05
G-protein signaling, adenylate cyclase activating pathway
                    153916    11540    AI465291    adenosine A2a receptor                                     0.159
heart development
                    989       14672    AI528620    guanine nucleotide binding protein, alpha 11               0.05
heavy metal ion transport
                    14926     11977    AI449437    ATPase, Cu++ transporting, alpha polypeptide               0.159
heparan sulfate proteoglycan metabolism
                    103788    27029    AI464451    calbindin 1, 28 kDa                                        0.05
humoral immune response
                    138544    16121    AI450390    immunoglobulin kappa chain variable 4 (V4)                 0.415
inflammatory response
                    12895     20299    AI449147    chemokine (C-C motif) ligand 22                            0.288
ion transport
                    3292      14810    AI385669    glutamate receptor, ionotropic, NMDA1 (zeta 1)             0.202
ionic insulation of neurons by glial cells
                    1268      18823    AI323793    proteolipid protein 1 (Pelizaeus-Merzbacher disease,       0.05
                                                   spastic paraplegia 2, uncomplicated)
iron homeostasis
                    7500      14325    AI449517    ferritin light chain 1                                     0.159
iron transport
                    7500      14325    AI449517    ferritin light chain 1                                     0.159
JAK-STAT cascade
                    38869     56469    AI448242    protein inhibitor of activated STAT 1                      0.05
lipid catabolism
                    1514      16956    AI326787    lipoprotein lipase                                         0.47
lipid metabolism
                    1514      16956    AI326787    lipoprotein lipase                                         0.415
lipid transport
                    1514      16956    AI326787    lipoprotein lipase                                         0.288
locomotory behavior
                    20964     14681    AI661491    guanine nucleotide binding protein, alpha o                0.159
lymph gland development
                    1715      16994    AI327398    lymphotoxin B                                              0.415
lysosomal lumen acidification
                    30155     11984    AI385732    ATPase, H+ transporting, V0 subunit C                      0.05
melanin biosynthesis, from tyrosine
                    19987     13190    AI325230    ATPase, Cu++ transporting, alpha polypeptide               0.05
mercury ion transport
                    14926     11977    AI449437    ATPase, Cu++ transporting, alpha polypeptide               0.05
mesoderm development
                    1424      14042    AI385657    exostoses (multiple) 1                                     0.05
metabotropic glutamate receptor signaling pathway
                    10022     26558    AI327089    homer homolog 3 (Drosophila)                                0.159
mitotic cycle control
                    18994     56321    AI426755    apoptosis antagonizing transcription factor                0.05
mRNA processing
                    28150     81898    AI666563    splicing factor 3b, subunit 1                              0.159
mRNA splice site selection
                    6787      20383    AI528616    splicing factor, arginine/serine-rich 3 (SRp20)            0.415
muscle contraction regulation
                    35134     11937    AI324248    ATPase, Ca++ transporting, cardiac muscle, fast twitch1    0.288
muscle development
                    1000      17901    AI324023    myosin light chain, alkali, fast skeletal muscle           0.415
neuroblast determination
                    10663     17172    AI415258    achaete-scute complex homolog-like 1 (Drosophila)          0.05
nitrogen fixation
                    2338      14645    AI413315    glutamate-ammonia ligase (glutamine synthase)              0.159
nucleosome assembly
                    193557    15269    AI323498    similar to germinal histone H4 gene                        0.288
one-carbon compound metabolism
                     3379      20425    AI452103    serine hydroxymethyl transferase 1 (soluble)               0.05
ossification
                     27757     12153    AI327151    bone morphogenetic protein 1                               0.05
oxygen transport*
                    30266     15129    AI323916    Hbb-b1 hemoglobin, beta adult major chain                  0.023
peptide hormone processing
                    4881      30052    AI604765    proprotein convertase subtilisin/kexin type 1 inhibitor    0.05
peptide metabolism*
                    5121      18484    AI323455    peptidylglycine alpha-amidating monooxygenase              0.035
peroxisome organization and biogenesis
                    20901     18632    AI596335    peroxisomal biogenesis factor 11b                          0.47
phototransduction
                    12925     18582    AI414297    phosphodiesterase 6D, cGMP-specific, rod, delta            0.159
proline biosynthesis
                    29751     56454    AI324071    pyrroline-5-carboxylate synthetase (glutamate              0.05
                                                   gamma-semialdehyde synthetase)
protein amino acid ADP-ribosylation
                    2816      11875    AI323430    ADP-ribosyltransferase 5                                   0.159
protein amino acid dephosphorylation
                    20253     54384    AI327236    myotubularin related protein 7                             0.055
protein amino acid glycosylation
                    10701     20452    AI385627    sialyltransferase 8 (alpha-2, 8-sialyltransferase) D       0.159
protein metabolism and modification
                    22271     80886    AI596338    similar to smt3-specific isopeptidase 1;                   0.159
                                                   sentrin/SUMO-specific protease
protein secretion
                    28375     53421    AI327023    SEC61, alpha subunit (S. cerevisiae)                       0.288
protein transport
                    27393     21855    AI429549    translocator of inner mitochondrial membrane b             0.371
protein-nucleus import, docking
                    16710     16211    AI323858    karyopherin (importin) beta 1                              0.159
purine nucleoside transport
                    29510     59023    AI413193    solute carrier family 28 (sodium-coupled nucleoside        0.05
                                                   transporter), member 2
RAS protein signal transduction
                    734       18176    AI414879    neuroblastoma ras oncogene                                 0.371
receptor mediated endocytosis
                    2735      65969    AI661835    SWI/SNF related, matrix associated, actin dependent        0.05
                                                   regulator of chromatin, subfamily d, member 1
regulation of body size
                    4132      12701    AI464459    suppressor of cytokine signaling 2                         0.159
regulation of cell migration
                    2453      20604    AI326805    somatostatin                                               0.05
retinoid metabolism
                    2450      19659    AI893623    retinol binding protein 1, cellular                        0.05
rhythmic behavior
                    10723     18628    AI428816    period homolog 3 (Drosophila)                              0.05
skeletal development
                    989       14672    AI528620    guanine nucleotide binding protein, alpha 11               0.05
SMAD protein heteromerization
                    7320      17127    AI324173    MAD homolog 3 (Drosophila)                                 0.159
SMAD protein nuclear translocation*
                    100399    17128    AI427147    MAD homolog 4 (Drosophila)                                 0.05
sodium transport
                    424       11933    AI450702    ATPase, Na+/K+ transporting, beta 3 polypeptide            0.288
spermatogenesis
                    4559      14598    AI323672    gamma-glutamyltransferase 1                                0.371
steroid biosynthesis
                    28099     20652    AI385523    sterol O-acyltransferase 1                                 0.159
steroid metabolism
                    5129      20905    AI430879    steroid sulfatase                                          0.05
transcription
                    27375     17749    AI661386    metallothionein-I activator                                0.159
transmembrane receptor protein tyrosine kinase signaling pathway
                    8534      13649    AI427644    epidermal growth factor receptor                           0.415
ubiquitin cycle
                    9002      22215    AI661496    ubiquitin protein ligase E3A                               0.415
vacuolar acidification
                    30155     11984    AI385732    ATPase, H+ transporting, V0 subunit C                      0.05
very long chain fatty acid metabolism
                    2567      54326    AI448451    elongation of very long chain fatty acids (FEN1/Elo2,      0.05
                                                   SUR4/Elo3, yeast)-like 2
water transport
                    40333     11831    AI452338    aquaporin 6                                                0.159
Wnt receptor signaling pathway
                    7883      11789    AI451571    adenomatosis polyposis coli                                0.05
xenobiotic metabolism
                    22637     64296    AI661482    RIKEN cDNA 0910001L24 gene                                 0.05

Wride, Mol Vis 2003; 9:360-396 <http://www.molvis.org/molvis/v9/a50/>
©2003 Molecular Vision <http://www.molvis.org/molvis/>
ISSN 1090-0535