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.
				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***

Berger et al. Lipids in Health and Disease 2006 5:10 doi:10.1186/1476-511X-5-10