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).

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

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

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

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

ASNS**        FUNCTION: asparagine synthase         Asparagine Biosynthesis               -
              (glutamine-hydrolyzing); glutamine
              amidotransferase; ligase. PROCESS:
              asparagine biosynthesis; glutamine
              metabolism; metabolism. COMPONENT:
              soluble fraction.

S62138        -                                     -                                     -

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:

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

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

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
                                                                                          cells, and in
                                                                                          the rough
                                                                                          reticulum. Also

GAPD          FUNCTION: glyceraldehyde              First step in the second phase of     Cytoplasmic
              3-phosphate dehydrogenase             glycolysis
              (phosphorylating); oxidoreductase.
              PROCESS: glycolysis. COMPONENT:

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

*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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