Table 4 of
Leung, Mol Vis 2003;
9:425-439.Table 4 of
Leung, Mol Vis 2003;
9:425-439.
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
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