Table 4 of
Leung, Mol Vis 2003;
Table 4. Gene ontology terms and SWISS-PROT annotations of differentially expressed genes
DEX induces differential expression for several genes. Here we provide the available Gene Ontology Terms and SWISS-PROT functions/pathways for these genes. Comparing the known functions of these genes with the effect of DEX on their expression allows us to formulate testable hypotheses that explain the mechanisms of action of DEX (Figure 4).
SWISS-PROT subcellular Symbol Gene ontology term* SWISS-PROT functions/pathways location ----------- ----------------------------------- ----------------------------------- --------------- GAS1 PROCESS: cell cycle arrest; A specific growth arrest protein Integral negative control of cell involved in growth suppression; membrane proliferation. blocks entry to s phase; prevents protein cycling of normal and transformed cells. CDH4 FUNCTION: calcium binding; Cadherins are calcium dependent Type i membrane calcium-dependent cell adhesion cell adhesion proteins. They protein molecule. PROCESS: transport; cell preferentially interact with adhesion; homophilic cell adhesion. themselves in a homophilic manner COMPONENT: plasma membrane; in connecting cells; cadherins may membrane. thus contribute to the sorting of heterogeneous cell types. May play an important role in retinal development. MT1L FUNCTION: heavy metal binding. Metallothioneins have a high - PROCESS: heavy metal sensitivity/ content of cysteine residues that resistance. bind various heavy metals; these proteins are transcriptionally regulated by both heavy metals and glucocorticoids. CST3 FUNCTION: cysteine protease As an inhibitor of cysteine - inhibitor; amyloid protein. proteinases, this protein is thought to serve an important physiological role as a local regulator of this enzyme activity. ATF4 FUNCTION: DNA binding; RNA This protein binds the camp Nuclear polymerase II transcription factor. response element (cre; consensus: PROCESS: transcription regulation. 5'gtgacgt(a/c)(a/g)-3'), a sequence COMPONENT: nucleus. present in many viral and cellular promoters. ASNS** FUNCTION: asparagine synthase Asparagine Biosynthesis - (glutamine-hydrolyzing); glutamine amidotransferase; ligase. PROCESS: asparagine biosynthesis; glutamine metabolism; metabolism. COMPONENT: soluble fraction. S62138 - - - (TLS/CHOP)* TLS FUNCTION: nucleic acid binding; DNA Binds both single-stranded and Nuclear binding; RNA binding. PROCESS: cell double-stranded DNA and promotes growth and/or maintenance. ATP-independent annealing of COMPONENT: nucleus. complementary single-stranded DNAs and D-Loop formation in superhelical double-stranded DNA. May Play a role in maintenance of genomic integrity. CHOP FUNCTION: transcription factor; Inhibits the DNA-binding activity Nuclear trancription co-repressor. PROCESS: of C/EBP and LAP by forming cell cycle control; transcription heterodimers that cannot bind DNA regulation; DNA damage response; cell cycle arrest; cell growth and/or maintenance. COMPONENT: nucleus HSPA5 FUNCTION: ATP binding; HSP70/ HSP90 Probably plays a role in Endoplasmic organizing protein. COMPONENT: facilitating the assembly of reticulum endoplasmic reticulum; endoplasmic multimeric protein complexes inside lumen reticulum lumen. the ER. TS11** FUNCTION: asparagine synthase Asparagine Biosynthesis - (glutamine-hydrolyzing); glutamine amidotransferase; ligase. PROCESS: asparagine biosynthesis; glutamine metabolism; metabolism. COMPONENT: soluble fraction. TSC22 FUNCTION: transcription factor. Transcriptional repressor. Acts on Nuclear and PROCESS: transcription regulation; the c-type natriuretic peptide cytoplasmic (by transcription from Pol II promoter. (cnp) promoter. similarity). COMPONENT: nucleus. LDHA FUNCTION: L-lactate dehydrogenase; Anaerobic glycolysis; final step. Cytoplasmic. oxidoreductase. PROCESS: glycolysis. COMPONENT: cytosol. IGFBP2 FUNCTION: insulin-like growth igf-binding proteins prolong the Secreted. factor receptor binding; plasma half-life of the igfs and have been protein; insulin-like growth factor shown to either inhibit or binding, growth factor binding. stimulate the growth promoting PROCESS: regulation of cell growth. effects of the igfs on cell COMPONENT: extracellular; culture. They alter the interaction extracellular space. of igfs with their cell surface receptors. TAGLN PROCESS: muscle development Actin cross-linking/gelling protein cytoplasmic (by similarity). Involved in (probable). calcium interactions and contractile properties of the cell that may contribute to replicative senescence. SCG2 FUNCTION: calcium binding. PROCESS: Secretogranin ii is a Neuroendocrine protein secretion. COMPONENT: neuroendocrine secretory granule and endocrine secretory vesicle protein, which is the precursor for secretory biologically active peptides. granules WARS FUNCTION: tRNA ligase; - - tryptophan-tRNA ligase; ATP binding; ligase. PROCESS: protein biosynthesis; amino acid activation; trytophanyl-tRNA aminocylation; negative control of cell proliferation. COMPONENT: soluble fraction; cytoplasm. MYOC FUNCTION: structural molecule. May participate in the obstruction Located PROCESS: vision; morphogenesis. of fluid outflow in the trabecular preferentially COMPONENT: non-muscle myosin; meshwork. in the ciliary cilium. rootlet and basal body of the connecting cilium of photoreceptor cells, and in the rough endoplasmic reticulum. Also secreted. GAPD FUNCTION: glyceraldehyde First step in the second phase of Cytoplasmic 3-phosphate dehydrogenase glycolysis (phosphorylating); oxidoreductase. PROCESS: glycolysis. COMPONENT: cytoplasm. ACTB FUNCTION: motor; structural Actins are highly conserved Cytoplasmic molecule; structural constituent of proteins that are involved in cytoskeleton. PROCESS: cell various types of cell motility and motility. COMPONENT: cytoskeleton; are ubiquitously expressed in all actin filament; actin cytoskeleton. eukaryotic cells PDHB FUNCTION: pyruvate dehydrogenase The pyruvate dehydrogenase complex Mitochondrial (lipoamide). PROCESS: glucose catalyzes the overall conversion of matrix metabolism; tricarboxylic acid pyruvate to acetyl-CoA and CO(2). cycle. COMPONENT: mitochondrion. It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3). *S62138 codes for a protein called TLS/CHOP, a hybrid protein produced by chromosome translocation in human myxoid liposarcoma **ASNS and TS11 have exactly the same sequence but repeatedly occurred in the database and array because they were annotated with different names