Table 2.
Expression Changes of 68 Selected Genes in Retinas of cbs+/− HM Mice
| Accession Number | Gene | Function | Change (x-Fold) |
|---|---|---|---|
| Proapoptosis Genes | |||
| NM_001085 409 | STEAP family member 3 (STEAP3) | p53 Signaling pathway | +3.34 |
| NM_057171 | HLA-B-associated transcript 3 (Bat3) | Regulator of apoptosis-inducing factor (AIF) stability in response to ER stress; regulator of p53 acetylation in response to DNA damage | +2.27 |
| NM_134062 | Death associated protein kinase 1 (Dapk1), transcript variant 2 | Tumor suppressor; p53 signaling pathway | +2.14 |
| NM_178590 | Inhibitor of kappaB kinase gamma (lkbkg), transcript variant 2 | CD40L signaling pathway; NF-κB signaling pathway; TNF/stress-related signaling; TNFR2 signaling pathway; Toll-like receptor pathway | −2.02 |
| NM_010721 | Lamin B1 (Lmnb1) | Caspase cascade in apoptosis; FAS signaling pathway (CD95); TNFR1 signaling pathway | −2.04 |
| NM_033217 | Nerve growth factor receptor (Ngfr) | Induces differentiation, tumor suppressor | −2.12 |
| NM_019752 | HtrA serine peptidase 2 (Htra2) | Promotes caspase-mediated apoptosis when dislocated from mitochondria | −2.20 |
| NM_008704 | Nonmetastatic cells 1, protein (NM23A) expressed in (Nme1) | Granzyme A mediated apoptosis pathway | −2.26 |
| NM_025562 | Fission 1 homolog (Fis1) | Mitochondrial fission; involved in intrinsic apoptosis pathways | −2.39 |
| Antiapoptosis Genes | |||
| NM_133752 | Optic atrophy 1 homolog (Opa1) | Mutated in dominant optic atrophy; role in mitochondrial fusion | +2.42 |
| NM_028844 | Aven | Caspase activation inhibitor; ATM activator in response to DNA damage | +2.31 |
| NM_009794 | Calpain 2 (Capn2) | Tumorigenic; regulator of autophagosome formation | +2.21 |
| NM_181585 | Phosphatidylinositol 3 kinase, regulatory subunit, polypeptide 3 (Pik3r3) | Tumorigenic via Akt pathway | −2.09 |
| NM_025816 | Tax1 (human T-cell leukemia virus type 1) binding protein 1 (Tax|bp|) | Inhibitor of TNF-induced apoptosis | −2.11 |
| NM_053245 | Aryl hydrocarbon receptor-interacting proteinlike 1 (Aip|1) | Negative regulator of apoptosis | −2.17 |
| NM_009688 | X-linked inhibitor of apoptosis (Xiap) | B-cell survival pathway; caspase cascade in apoptosis | −2.19 |
| NM_030152 | Nucleolar protein 3 (Nol3) | Inhibitor of caspase cascade | −2.19 |
| NM_011361 | Serum/glucocorticoid regulated kinase 1 (Sgk1) | Protective during oxidative stress and neurodegeneration | −2.22 |
| NM_029922 | Poly (ADP-ribose) polymerase family, member 6 (Parp6) | Regulates telomere elongation | −2.23 |
| NM_026669 | Testis enhanced gene transcript (Tegt) | Inhibitor of Bax | −2.32 |
| NM_009429 | Tumor protein, translationally-controlled 1 (Tpt1) | Antagonizes bax function | −2.44 |
| NM_009689 | Baculoviral IAP repeat-containing 5 (Birc5) | B-cell survival pathway (Survivin) | −2.84 |
| NM_011810 | Fas apoptotic inhibitory molecule (Faim) | Inhibits Fas activity | −2.94 |
| Genes Involved in Cell Cycle | |||
| NM_007913 | Early growth response 1 (Egr1) | Downregulates the MAP kinase pathway; positive correlation with NMDA receptor stimulation | +4.73 |
| NM_145221 | Adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1 (App11) | Regulator of Akt activity | +2.39 |
| NM_019726 | G protein pathway suppressor 2 (Gps2) | GTPase inhibitor activity; facilitates p53 activity; has been shown to interact with NR3 subunit of NMDA receptor | +2.17 |
| NM_001010 833 | Mediator of DNA damage checkpoint 1 (Mdc1) | Regulates intra-S phase checkpoint in response to DNA damage | +2.03 |
| NM_028023 | Cell division cycle associated 4 (Cdca4) | Regulates cell proliferation via E2F/Rb pathway | −2.00 |
| NM_019712 | Ring-box 1 (Rbx1) | ER-associated degradation (ERAD) pathway; regulation of p27 phosphorylation during cell cycle progression | −2.01 |
| NM_019830 | Protein arginine N-methyltransferase 1 (Prmt1) | BTG family proteins and cell cycle regulation; control of gene expression by vitamin D receptor | −2.04 |
| NM_053089 | NMDA receptor-regulated gene 1 (Narg1) | N-terminal acetyltransferase that regulates entry into G0 phase of cell cycle; downregulated by NMDA receptor function | −2.05 |
| NM_011959 | Origin recognition complex, subunit 5-like (Orc5|) | CDK Regulation of DNA Replication | −2.16 |
| NM_008228 | Histone deacetylase 1 (Hdac1) | Deacetylation of histones; chromatin modification | −2.20 |
| NM_007836 | Growth arrest and DNA-damage-inducible 45 alpha (Gadd45a) | ATM signaling pathway; cell cycle: G2/M checkpoint; p53 signaling pathway | −2.31 |
| NM_008683 | Neural precursor cell expressed, developmentally downregulated gene 8 (Nedd8) | Regulation of p27 Phosphorylation during Cell Cycle Progression | −2.43 |
| NM_007631 | Cyclin D1 (Ccnd1) | BTG family proteins and cell cycle regulation; cell cycle: G1/S check point; cyclins and cell cycle regulation; inactivation of Gsk3 by AKT causes accumulation of b-catenin in alveolar macrophages; influence of Ras and Rho proteins on G1 to S transition | −2.66 |
| NM_007691 | Checkpoint kinase 1 homolog (Chek1) | ATM signaling pathway; cdc25 and chk1 regulatory pathway in response to DNA damage; cell cycle: G2/M checkpoint; RB tumor suppressor/checkpoint signaling in response to DNA damage; role of BRCA1, BRCA2, and ATR in cancer susceptibility | −3.27 |
| NM_010730 | Annexin A1 (Anxa1) | Anti-inflammatory action; proapoptotic upon upregulation; mediates phagocytosis of apoptotic cells | −4.93 |
| Genes with Antioxidant Activity | |||
| NM_025823 | Prenylcysteine oxidase 1 (Pcyox1) | Oxidoreductase activity; prenylcysteine catabolic process | +2.85 |
| NM_145598 | Nucleoredoxin-like 1 (Nxnl1) | Cell redox homeostasis | −2.03 |
| NM_010358 | Glutathione S-transferase, mu 1 (Gstm1) | Glutathione metabolism; metabolism of xenobiotics by cytochrome P450 | −2.03 |
| NM_013711 | Thioredoxin reductase 2 (Txnrd2) | Mitochondrial redox homeostasis | −2.04 |
| NM_013541 | Glutathione S-transferase, pi 1 (Gstp1) | Glutathione metabolism | −2.13 |
| NM_008185 | Glutathione S-transferase, theta 1 (Gstt1) | Glutathione metabolism | −2.28 |
| NM_010357 | Glutathione S-transferase, alpha 4 (Gsta4) | Glutathione metabolism | −2.58 |
| NM_011435 | Superoxide dismutase 3, extracellular (Sod3) | Antioxidant activity | −2.61 |
| NM_025569 | Microsomal glutathione S-transferase 3 (Mgst3) | Glutathione metabolism | −2.68 |
| NM_010362 | Glutathione S-transferase omega 1 (Gsto1) | Glutathione metabolism | −5.18 |
| Genes Associated with Calcium Signaling | |||
| NM_172152 | Solute carrier family 24 (sodium/potassium/calcium exchanger), member 4 (Slc24a4) | Calcium ion antiporter | +3.36 |
| NM_133741 | SNF-related kinase (Snrk) | Calcium regulated Ser/Thr kinase; involved in low K+-induced neuronal apoptosis | +3.09 |
| NM_080465 | Potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2 (Kcnn2) | Calcium activated potassium channel activity; calmodulin binding | +2.96 |
| NM_001039 139 | Calcium/calmodulin-dependent protein kinase II gamma (Camk2g) | Calcium signaling pathway; ErbB signaling pathway; Glioma; GnRH signaling pathway; Long-term potentiation; melanogenesis; olfactory transduction; Wnt signaling pathway | +2.52 |
| NM_001036 684 | ATPase, Ca++ transporting, plasma membrane 2 (Atp2b2) | Calcium signaling pathway | +2.51 |
| NM_007451 | Solute carrier family 25 (mitochondrial carrier, adenine nucleotide translocator), member 5 (Slc25a5) | Calcium signaling pathway | −2.21 |
| NM_009112 | S100 calcium binding protein A10 (calpactin) (S100a10) | Calciumion binding | −2.23 |
| NM_007590 | Calmodulin 3 (Calm3) | Encodes a subunit of calmodulin, primary Ca+ binding protein | −2.24 |
| NM_011636 | Phospholipid scramblase 1 (Plscr1) | Calcium ion binding | −8.33 |
| Genes Related to Axon Growth | |||
| NM_007911 | Ephrin B3 (Efnb3), mRNA | Axon guidance | +2.69 |
| NM_177678 | Actin-binding LIM protein 2 (Ablim2) | Axon guidance | +2.66 |
| NM_001039 363 | Tuberous sclerosis 2 (Tsc2) | Control of gene expression by vitamin D receptor; mTOR signaling pathway; suppressor of axon formation | +2.53 |
| NM_016890 | Dynactin 3 (Dctn3) | Essential for axon growth cone advance; microtubule-associated complex | −2.10 |
| Miscellaneous | |||
| NM_011701 | Vimentin (Vim) | Cell communication; intermediate filament | −3.03 |
| NM_008806 | Phosphodiesterase 6B, cGMP, rod receptor, beta polypeptide (Pde6b) | 3′,5′-cyclic-GMP-phosphodiesterase activity; detection of light stimulus | −3.41 |
| NM_019439 | Gamma-aminobutyric acid (GABA-B) receptor 1 (Gabbr1) | Neuractive ligand-receptor interaction | −3.95 |
| NM_009089 | Polymerase (RNA) II (DNA directed) polypeptide A (Polr2a) | Chromatin remodeling by hSW1/SNF ATP-dependent complexes; nuclear receptors coordinate the activities of chromatin remodeling complexes and coactivators to facilitate initiation of transcription in carcinoma cells; repression of pain sensation by the Tr | −4.59 |
| NM_013697 | Transthyretin (Ttr) | Carrier protein for thyroxine and retinol binding protein | −7.13 |
| NM_207028 | Taste receptor, type 2, member 126 (Tas2r126) | Taste transduction | −7.25 |
| NM_033614 | Phosphodiesterase 6C, cGMP-specific, cone, alpha prime (Pde6c) | 3′,5′-cyclic-GMP-phosphodiesterase activity | −7.76 |
q < 0.06 for all genes included (n = 5 wild-type, 5 cbs+/− HM mice). GenBank accession numbers provided by NCBI (Bethesda, MD; http://www.ncbi.nlm.nih.gov/Genbank).