Table 3 Genes differentiating FUNG, FISH, AND COMB. Genes differentiating FUNG, FISH, and COMB. Shown are genes differentiating each group from all other groups, for which annotations were available. Unigene numbers lack Mm. prefix. Fold changes, relative to the differentiating group, are as follows: red, up regulation; green, down regulation. For example, for tcfe3, COMB was the differentiating group. Transcript levels for tcfe3 were 6.2 fold less for COMB relative to CONT; 7.8 fold less for COMB relative to FUNG; and 11.1 fold less for COMB relative to FISH; and FISH increased transcript levels relative to FUNG. Biological categories (e.g., Structural Role, Phosphatases and kinases) were derived from gene ontology (GO) nomenclature. Within each biological category, rows were sorted by differentiating group (FUNG, FISH, COMB), up or down regulation, and thereafter, alphabetically. ***P≤0.001; **0.001<P≤0.005; *0.005<P≤0.010. A more extensive version of this table including GO biological processes and GO molecular functions is available upon request.
| Â | Â | Â | Â | Fold Change: Differentiating group vs. other groups: | |||
|---|---|---|---|---|---|---|---|
Gene Symbol | Name | Unigene | Differentiating Group | CONT | FUNG | FISH | COMB |
Structural role (adhesion, microtubule, actin) | |||||||
Sn | sialoadhesin | 1374 | COMB | -2.7*** | -2.6** | -2.8*** | Â |
Catns | catenin src | 198356 | FUNG | -1.5* | Â | -1.7** | -1.6* |
Diaph1 | diaphanous homolog 1 (Drosophila) | 3282 | FUNG | -3.5*** | Â | -4.9*** | -4.2*** |
acta2 | actin, alpha 2, smooth muscle, aorta | 16537 | COMB | -3.9*** | -5.0*** | -4.9*** | Â |
arhgef7 | Rho guanine nucleotide exchange factor (GEF7) | 3439 | COMB | -3.4** | -3.7** | -3.8** | Â |
cryaa | crystallin, alpha A | 1228 | FISH | -2.8*** | -3.1** | Â | -4.7*** |
homer2 | homer homolog 2 (Drosophila) | 228 | FISH | -60.5*** | -50.5*** | Â | -68.9*** |
tubb2 | tubulin, beta 2 | 246377 | COMB | -3.6*** | -2.2** | -3.8*** | Â |
tubb3 | tubulin, beta 3 | 40068 | COMB | -2.7*** | -2.0** | -2.9*** | Â |
eln | elastin | 111845 | FUNG | -19.0** | Â | -16.6* | -19.1* |
dvl2 | dishevelled 2, dsh homolog (Drosophila) | 5114 | FISH | -29.4*** | -47.3** | Â | -21.9* |
numbl | numb-like | 49224 | FUNG | -27.3*** | Â | -58.3*** | -22.9*** |
hps1 | Hermansky-Pudlak syndrome 1 homolog (human) | 218381 | COMB | -3.3*** | -3.2** | -3.7*** | Â |
plod3 | procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 | 137885 | FUNG | -4.7*** | Â | -5.2*** | -4.5*** |
hip1r | huntingtin interacting protein 1 related | 149954 | COMB | -9.1*** | -8.2** | -7.0** | Â |
Phosphatases and kinases | |||||||
ppp1ca | protein phosphatase 1, catalytic subunit, alpha isoform | 1970 | FUNG | -18.5*** | Â | -12.3*** | -23.4*** |
ppp2cb | protein phosphatase 2a, catalytic subunit, beta isoform | 7418 | FISH | 1.9*** | 1.6* | Â | 1.9*** |
ppm1b | protein phosphatase 1B, magnesium dependent, beta isoform | 849 | FISH | -27.4** | -48.3*** | Â | -57.5*** |
ptpn1 | protein tyrosine phosphatase, non-receptor type 1 | 2668 | FUNG | -10.3*** | Â | -28.4*** | -13.3*** |
dusp1 | dual specificity phosphatase 1 | 2404 | COMB | -2.2** | -3.2*** | -2.6*** | Â |
dusp9 | dual specificity phosphatase 9 | 16479 | COMB | -53.8*** | -34.1*** | -70.8*** | Â |
camk2b | calcium/calmodulin-dependent protein kinase II, beta | 4857 | FISH | -8.8*** | -8.6*** | Â | -4.5** |
ptpra | protein tyrosine phosphatase, receptor type, A | 587 | COMB | -10.2*** | -12.2** | -8.0* | Â |
fgfr3 | fibroblast growth factor receptor 3 | 6904 | FISH | -3.3** | -3.7** | Â | -3.3* |
plk1 (plk) | polo-like kinase homolog, (Drosophila) | 16525 | COMB | -1.9*** | -2.1*** | -2.0*** | Â |
ccnb1 | cyclin B1 | 22569 | FUNG | -46.7*** | Â | -19.5*** | -58.6*** |
cdk4 | cyclin-dependent kinase 4 | 6839 | FISH | -2.8*** | -2.5** | Â | -3.4*** |
ntrk1 | neurotrophic tyrosine kinase, receptor, type 1 | 129850 | COMB | -2.84*** | -3.31*** | -3.7*** | Â |
G protein coupled signaling | |||||||
rgs16 | regulator of G-protein signaling 16 | 181709 | COMB | 2.2*** | 1.9* | 2.9*** | Â |
gnat1 | guanine nucleotide binding protein, alpha transducing 1 | 69061 | COMB | -20.4*** | -18.8*** | -17.9** | Â |
Transcription factors | |||||||
notch2 | Notch gene homolog 2, (Drosophila) | 57005 | FUNG | -5.0*** | Â | -6.6*** | -3.4* |
barx1 | BarH-like homeobox 1 | 42241 | FUNG | -23.5*** | Â | -62.5*** | -15.1*** |
tcfeb (tfeb) | transcription factor EB | 2305 | FUNG | -4.3*** | Â | -6.5*** | -5.1*** |
nfkbia | nuclear factor of kappa light chain gene enhancer in B-cells inhibitor, alpha | 8884 | FISH | -1.6** | -2.1*** | Â | -1.9*** |
jund1 | Jun proto-oncogene related gene d1 | 1175 | FISH | -7.2** | -18.6*** | Â | -14.0*** |
jun | Jun oncogene | 482 | FISH | -4.7*** | -5.5*** | Â | -4.2*** |
yy1 | YY1 transcription factor | 3868 | FISH | -3.2*** | -5.7*** | Â | -4.4*** |
tef | thyrotroph embryonic factor | 19258 | FISH | -21.9*** | -18.4** | Â | -24.2** |
usf2 | upstream transcription factor 2 | 15781 | FISH | -5.6*** | -6.9*** | Â | -5.5*** |
hoxa13 | homeo box A13 | 8056 | FISH | -2.5*** | -2.2* | Â | -2.6** |
tcea2 | transcription elongation factor A (SII), 2 | 24245 | FISH | -8.7** | -16.8*** | Â | -33.3*** |
foxa3; hnf-3g | forkhead box A3 | 42260 | COMB | -2.2*** | -2.8*** | -2.4*** | Â |
tcf7 | transcription factor 7, T-cell specific | 31630 | COMB | 2.5** | 2.1* | 2.6** | Â |
tcf2 | transcription factor 2 | 7226 | COMB | -55.0*** | -46.5*** | -89.1*** | Â |
atf5 | activating transcription factor 5 | 1566 | COMB | -3.1*** | -1.9*** | -2.0*** | Â |
gtf2i | general transcription factor II I | 22593 | COMB | -11.4*** | -6.8** | -20.6*** | Â |
asb6 | ankyrin repeat and SOCS box-containing protein 6 | 27656 | COMB | -20.8*** | -13.3** | -16.0*** | Â |
mllt1 | myeloid/lymphoid or mixed lineage-leukemia translocation to 4 homolog (Drosophila) | 148748 | COMB | -9.8*** | -15.0*** | -12.2*** | Â |
ighmbp2 | immunoglobulin mu binding protein 2 | 3179 | COMB | -5.3*** | -4.3* | -6.3*** | Â |
nr2c2 | nuclear receptor subfamily 2, group C, member 2 | 3535 | COMB | -37.9*** | -81.7*** | -19.72*** | Â |
tcfe3 (tfe3) | transcription factor E3 | 25762 | COMB | -6.2*** | -7.8*** | -11.1*** | Â |
miz1 (pias2) | Msx-interacting-zinc finger | 6370 | COMB | -1.9* | -3.3*** | -2.9*** | Â |
jmj | jumonji | 25059 | COMB | -8.7*** | -14.6*** | -7.1** | Â |
mRNA and rRNA splicing and processing | |||||||
sf3a2 | splicing factor 3a, subunit 2, 66kD | 34039 | FUNG | 1.6** | Â | 2.0*** | 1.7** |
nono | non-POU-domain-containing, octamer binding protein | 21559 | FUNG | -4.6*** | Â | -6.2*** | -10.6*** |
srp9 | signal recognition particle 9 kDa | 89927 | COMB | -3.1** | -2.7* | -3.3** | Â |
bop1 | block of proliferation 1 | 4283 | FISH | -10.1* | -11.9* | Â | -14.0* |
zfp385 (znf385) | zinc finger protein 385 | 14099 | COMB | -2.3*** | -2.3*** | -1.7** | Â |
Amino acid and protein metabolism | |||||||
dct | dopachrome tautomerase | 19987 | FUNG | -4.8*** | Â | -4.5*** | -2.1*** |
mrpl23 | mitochondrial ribosomal protein L23 | 12144 | COMB | -16.4*** | -13.9*** | -18.7*** | Â |
rpl28 | ribosomal protein L28 | 3111 | COMB | -1.8*** | -1.5** | -1.8*** | Â |
eef2 | eukaryotic translation elongation factor 2 | 27818 | FISH | -4.9*** | -3.0*** | Â | -4.0*** |
eef1a1 (2 probes) | eukaryotic translation elongation factor 1 alpha 1 | 196614 | FUNG | -1.6*** to -1.7*** | Â | -1.6** to -2.1*** | -1.5* to -1.9*** |
eprs | glutamyl-prolyl-tRNA synthetase | 154511 | COMB | -16.2*** | -17.3*** | -18.9*** | Â |
sars1 | seryl-aminoacyl-tRNA synthetase 1 | 28688 | FISH | -4.5*** | -4.5** | Â | -4.2* |
ppil2 | peptidylprolyl isomerase (cyclophilin)-like 2 | 218627 | COMB | -3.4*** | -4.6*** | -3.7*** | Â |
ywhaq | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide | 14722 | FUNG | -4.0** | Â | -4.4* | -7.3*** |
oat | ornithine aminotransferase | 13694 | FUNG | 1.7*** | Â | 1.5* | 1.7*** |
lamp2 | lysosomal membrane glycoprotein 2 | 486 | FUNG | -12.7*** | Â | -15.6*** | -45.0*** |
ang | angiogenin (2 probes) | 202665 | FISH | -1.5* to -2.7*** | -1.8*** to -4.5*** | Â | -1.8*** to -2.1* |
kai1 (cd82) | kangai 1 (suppression of tumorigenicity 6, prostate) | 4261 | FISH | -1.7*** | -2.3*** | Â | -1.5* |
psmb10 | proteasome (prosome, macropain) subunit, beta type 10 | 787 | FISH | -22.7*** | -47.8*** | Â | -14.0** |
folh1 | folate hydrolase | 7522 | FUNG | -10.8** | Â | -13.3* | -21.1** |
mcpt7 (tpsab1) | mast cell protease 7 | 3301 | COMB | -3.5*** | -2.9*** | -3.5*** | Â |
Lipid metabolism and P450s | |||||||
acas2 | acetyl-Coenzyme A synthetase 2 (ADP forming) | 22719 | COMB | -4.8*** | -2.0* | -2.9*** | Â |
scd1 (2 probes) | stearoyl-Coenzyme A desaturase 1 | 140785 | COMB | -1.5** to -1.8*** | -1.4* to -1.7*** | -1.6*** to -1.7*** | Â |
elovl3; cig30 | elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 3 | 21806 | FISH | 1.9*** | 2.2*** | Â | 3.4*** |
fasn | fatty acid synthase | 3760 | FUNG | -1.8*** | Â | -1.4* | -3.2*** |
acly (2 probes) | ATP citrate lyase (ACL) | 25316 | COMB | -3.6 to -5.2*** | -1.9 to -2.0*** | -2.0 to -2.3*** | Â |
lypla3 | lysophospholipase 3 | 25492 | FISH | -32.4*** | -25.9*** | Â | -23.9*** |
thrsp | thyroid hormone responsive SPOT14 homolog (Rattus) | 28585 | COMB | -1.8*** | -2.3*** | -1.7*** | Â |
cyp4a10 | cytochrome P450, 4a10 | 10742 | FISH | 4.7*** | 1.7** | Â | 1.7** |
cyp24 | cytochrome P450, 24 | 6575 | FUNG | -8.6** | Â | -15.1*** | -19.3*** |
Carbohydrate metabolism | |||||||
lgals3 | lectin, galactose binding, soluble 3 | 2970 | FUNG | -4.0*** | Â | -5.5*** | -4.8*** |
idua | iduronidase, alpha-L- | 3054 | COMB | -14.7*** | -15.7*** | -12.2** | Â |
gaa | glucosidase, alpha, acid | 4793 | COMB | -3.1*** | -2.5** | -2.3** | Â |
g6pc | glucose-6-phosphatase, catalytic | 18064 | COMB | -1.9*** | -2.3*** | -3.0*** | Â |
pkm2 | pyruvate kinase, muscle | 2635 | FISH | -23.3*** | -48.8*** | Â | -12.2** |
bat2 | HLA-B associated transcript 2 | 20304 | COMB | -9.6*** | -4.8** | -7.7*** | Â |
Transport (lipid and other) | |||||||
abce1 | ATP-binding cassette, sub-family E (OABP), member 1 | 5831 | FISH | 2.7*** | 2.5** | Â | 2.5** |
fabp5 | fatty acid binding protein 5, epidermal | 741 | FISH | -12.1*** | -2.0** | Â | -1.8*** |
hspg2 | perlecan (heparan sulfate proteoglycan 2) | 7257 | COMB | -6.7*** | -5.5*** | -3.5** | Â |
dbi | diazepam binding inhibitor | 2785 | COMB | -1.4** | -1.5** | -1.8*** | Â |
cd36 | CD36 antigen | 18628 | FISH | 2.4*** | 2.5*** | Â | 3.8*** |
rab5c | RAB5C, member RAS oncogene family | 29829 | FISH | -3.6*** | -3.6*** | Â | -4.0*** |
ap4s1 | adaptor-related protein complex AP-4, sigma 1 | 116858 | FUNG | -24.3* | Â | -54.2*** | -22.6* |
slc4a2 | solute carrier family 4 (anion exchanger), member 2 | 4580 | FUNG | 3.0** | Â | 3.9** | 5.3*** |
slc10a1 | solute carrier family 10 (sodium/bile acid cotransporter family), member 1 | 104295 | FISH | -1.6** | -1.7** | Â | -1.7** |
apoc1 | apolipoprotein C-I | 182440 | FUNG | -1.6*** | Â | -1.7*** | -1.5** |
apoe | apolipoprotein E | 156335 | FISH | 1.5*** | 1.4* | Â | 1.8*** |
slc27a1 | solute carrier family 27 (fatty acid transporter), member 1 | 7206 | FUNG | -2.0** | Â | -2.2** | -2.3** |
apoa4 | apolipoprotein A-IV | 4533 | COMB | -17.2*** | -7.0*** | -5.4*** | Â |
hba-a1 | hemoglobin alpha, adult chain 1 | 196110 | FISH | 1.5*** | 1.4* | Â | 2.0*** |
hbb-b1 | hemoglobin, beta adult major chain | 233825 | COMB | -1.7*** | -1.7*** | -2.3*** | Â |
aqp8 | aquaporin 8 | 9970 | COMB | -3.6*** | -1.7** | -1.7** | Â |
Immune response/oxidative stress | |||||||
c5r1 | complement component 5, receptor 1 | 137488 | FISH | -79.3*** | -165.2*** | Â | -87.7*** |
cd72 | CD72 antigen | 88200 | FISH | -46.2*** | -38.9** | Â | -41.1** |
aldh1a7 | aldehyde dehydrogenase family 1, subfamily A7 | 14609 | FISH | 1.9*** | 1.6** | Â | 1.6** |
mif | macrophage migration inhibitory factor | 2326 | FISH | -2.3*** | -3.1*** | Â | -1.9*** |
prdx2 | peroxiredoxin 2 | 42948 | FISH | -1.6*** | -1.7** | Â | -1.6** |
hspb1 | heat shock protein 1 | 13849 | FISH | -4.0*** | -5.8*** | Â | -6.3*** |
hspcb | heat shock protein 1, beta | 2180 | FUNG | -1.5* | Â | -1.6* | -1.7** |
hpxn | hemopexin | 3485 | COMB | -1.5*** | -1.9*** | -1.5** | Â |
Heme synthesis | |||||||
alas1 | aminolevulinic acid synthase 1 | 19143 | FUNG | 3.9*** | Â | 2.1*** | 1.6** |
alas2 | aminolevulinic acid synthase 2, erythroid | 140509 | FUNG | -2.7** | Â | -2.9** | -2.8** |
Calcium, sodium, zinc ion binding | |||||||
tpt1 | tumor protein, translationally-controlled 1 | 254 | FUNG | -1.6** | Â | -1.7** | -1.6* |
fxyd2 | FXYD domain-containing ion transport regulator 2 | 22742 | COMB | -29.9*** | -57.5*** | -20.8* | Â |
zfp312 | zinc finger protein 312 | 34644 | FISH | -6.0* | -8.2* | Â | -12.8** |
slc30a3 | solute carrier family 30 (zinc transporter), member 3 | 1396 | FISH | -4.2** | -5.3** | Â | -6.8*** |
s100a3 | S100 calcium binding protein A3 | 703 | COMB | -3.0*** | -4.0*** | -4.4*** | Â |
rhbdl4 | rhomboid like gene 4 (Drosophila) | 219535 | FISH | -3.3** | -4.3*** | Â | -3.4** |
Miscellaneous | |||||||
serpinc1 | serine (or cysteine) proteinase inhibitor, clade C (antithrombin), member 1 | 30025 | FISH | 1.7*** | 1.8*** | Â | 2.5*** |
ssr2 | signal sequence receptor, beta | 7091 | FUNG | -5.0*** | Â | -8.0*** | -5.5** |
ssr1 | signal sequence receptor, alpha | 138725 | FISH | -6.2*** | -5.9*** | Â | -6.3*** |
surf1 | surfeit gene 1 | 6874 | FISH | -2.4*** | -2.4** | Â | -2.3** |
wbp1 | WW domain binding protein 1 | 1109 | FISH | -3.9*** | -2.6*** | Â | -3.5*** |