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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.

From: How dietary arachidonic- and docosahexaenoic- acid rich oils differentially affect the murine hepatic transcriptome

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