Tables
- Profiling of chicken adipose tissue gene expression by genome array

Table 1

BW, AFW and AFP of chickens used in the study

	Fat line	Lean line

	7-3-3	7-3-8	7-3-15	7-3-16	7-3-24	7-1-1	7-1-2	7-1-4	7-1-11	7-1-17
BW(g)	2690	2615	2915	2940	2895	2655	2655	2080	2375	2685
AFW(g)	103.4	116.6	115.3	112.1	138.4	36.91	40.13	28.27	23.46	40.83
AFP (%)	3.84	4.46	3.96	3.81	4.78	1.39	1.51	1.36	0.99	1.52

Table 2

Some highly expressed genes in chicken adipose tissue at 7 weeks

	The signal intensity analyzed by scanner
Genes	Fat line	Lean line

	7-3-3	7-3-8	7-3-15	7-3-16	7-3-24	7-1-1	7-1-2	7-1-4	7-1-11	7-1-17

A-FABP	44732	47715	46157	57201	52558	52286	49813	51861	50529	47910
spot 14	33917	30120	28795	35261	36359	19983	25819	24245	31674	31015
LPL	27133	24469	29421	25855	30799	18393	20950	23462	25275	23246
IGFBP-7	20471	22532	21163	27799	24675	24113	25764	29104	26375	28610
BMP7	29042	30313	25289	25124	22610	15932	24165	13953	26518	33345
hsp70	33480	32478	30641	21373	23217	19213	21624	16512	21503	30312
PCHK23	21402	19941	19423	30817	30956	29866	25764	24882	22561	25995
hsp25	32908	19470	23662	21037	25644	19327	7967	22002	19564	27742
glutathione peroxidase 4	22459	21447	24945	23085	24229	18705	23685	27400	27560	24096
stem cell antigen 2	32224	31256	22169	24894	26446	21403	27675	24483	26370	26105
CD74 gene	45284	38191	36116	38875	37099	43381	38466	32027	40065	39493
Vimentin	38624	36822	37965	33403	35772	36159	40251	41728	40184	40972
ubiquitin C	42501	37306	45125	39121	35707	35202	40535	42767	43055	41982
Thymosin beta 4	35340	33804	38768	34644	30105	42836	37625	34939	36087	37120
MCH II antigen B-L Beta	32147	29581	28406	34359	28741	38580	30089	29337	28674	31680
T-cell leukemia, homeobox 3	26240	29169	34325	24093	24060	36533	29476	28294	28493	31986
platelet/endothelial cell adhesion molecule	21515	16459	10731	12262	13868	16684	18476	17751	14270	17975

Table 3

Some poorly expressed genes in chicken adipose tissue at 7 weeks

	The signal intensity analyzed by scanner
Genes	Fat line	Lean line

	7-3-3	7-3-8	7-3-15	7-3-16	7-3-24	7-1-1	7-1-2	7-1-4	7-1-11	7-1-17

IGF-I	5.7	11.3	91	7	5.8	52	27.6	22.7	46.6	91.6
UCP	43.3	87.1	104.2	130	119.4	122.2	818.2	289.2	159.6	150.6
APOVLDLII	140.1	103	75.8	107.3	156.2	298.3	72.5	22.6	143.8	98.4
L-FABP	57.7	70.6	126.9	32.6	128.3	623.8	844.5	88.8	52.4	4865
TGFa	115.1	216.8	79.8	51	94.3	186.6	37.7	49.7	166.1	95.8
TGFβR	82.3	151.7	83.3	153.6	146	279.6	166.3	221.9	140.6	191.4
PEPCK-M	503.8	206.3	326	38.1	117.3	404.2	154.2	150.5	140	198.6
BMP2	236	355.4	262.7	317.2	430.9	209.3	399.6	228.6	337	208.6
acetyl-coenzyme A carboxylase alpha	232.5	181.8	319.5	396.4	172.9	181.7	160.8	207.1	144.9	111.8
type I TGF β receptor	82.3	146	153.6	83.3	151.7	191.4	140.6	221.9	279.6	166.3
cAMP response element- binding protein	96.9	115.5	132.3	75	146.5	171.6	91	82.7	196.4	132.6
hexokinase 2 (HK2)	270.3	458.9	526.4	779.8	287.3	523	471.5	337.2	294.7	398.3
Proinsulin	263	269.5	361	540.1	293	336	311	411.1	422.6	190.2
GDF-9	198.1	197.8	216.7	413	190.7	246.8	151.7	110.6	262.9	147.2
BMP5	216.3	382.1	179.5	241.8	257.8	132.2	282.2	264.5	173	288.6
mitogen-activated protein kinase phosphatase 2	231.5	288.2	247.1	238.6	280.5	239.6	136.8	415.3	300.7	205.1
(MKP-2) riboflavin-binding protein	239.7	17.6	179	75.8	242.5	139.8	424.4	60.8	129.9	291.4

Table 4

Some "not expressed" genes in adipose tissue of 7-week-old chickens

Probe set ID	Genes	mismatching probes pairs/the total probes pairs^a

Gga.10702.1.A1_at	insulin-like growth factor 2	10/10
Gga.11305.1.S1_s_at	thyroid hormone receptor associated protein 2	10/10
Gga.11817.1.S1_s_at	apolipoprotein B	10/10
Gga.12348.2.S1_a_at	glycosyltransferase	10/10
Gga.13.1.S1_s_at	leptin receptor	10/10
Gga.4123.1.S1_at	lipoprotein (APOVLDLII)	10/10
Gga.1731.1.S1_at	pyruvate carboxylase	10/10
Gga.742.1.S1_at	somatostatin-14	10/10
Gga.1267.1.S1_a_at	growth hormone 1	10/10
Gga.560.1.S1_at	growth differentiation factor 8	10/10
Gga.5646.2.S1_at	diacylglycerol kinase, zeta 104 kDa	10/10
GgaAffx.21833.1.S1_s_at	cholecystokinin receptor	10/10
GgaAffx.21834.1.S1_s_at	cholecystokinin	10/10
GgaAffx.21846.1.S1_s_at	transforming growth factor alpha	10/10
GgaAffx.2229.1.S1_at	polyamine oxidase (exo-N4-amino)	10/10
Gga.579.1.S1_at	neurotrophic tyrosine kinase, receptor, type 1	10/10
Gga.609.1.S1_at	thyroid hormone receptor beta 2	10/10
Gga.151.1.S1_at	sterol regulatory element binding transcription factor 1	10/10
Gga.686.1.S1_at	bone morphogenetic protein 4	10/10
Gga.689.1.S1_at	low density lipoprotein-related protein 1	10/10
Gga.15741.1.S1_at	growth arrest-specific 2	10/10
Gga.16782.1.S1_at	phosphoinositide-3-kinase, catalytic	10/10
Gga.761.1.S1_at	Mel-1c melatonin receptor	10/10
Gga.762.1.S1_at	melatonin receptor 1	10/10
Gga.784.1.S1_at	protein-tyrosine phosphatase CRYPalpha	10/10
Gga.793.1.S1_s_at	acetylcholinesterase	10/10
Gga.811.1.S1_at	growth differentiation factor 2	10/10
Gga.17381.1.S1_at	phospholipase C-like 3	10/10
Gga.857.1.S1_at	epidermal growth factor receptor	10/10
Gga.6214.1.S1_a_at	phospholipase A2, group IB (pancreas)	10/10
Gga.3663.2.S1_at	nucleolin	10/10
Gga.3707.2.A1_at	CCAAT/enhancer binding protein (C/EBP), gamma	10/10
GgaAffx.2229.1.S1_at	polyamine oxidase (exo-N4-amino)	10/10
GgaAffx.3695.1.S1_s_at	myelin transcription factor 1	10/10
GgaAffx.3803.6.S1_at	plexin A1	10/10
Gga.2645.1.S1_at	transforming growth factor, beta receptor II	10/10
Gga.2694.1.S1_at	lymphoid enhancer-binding factor 1	10/10
Gga.271.1.A1_at	bone morphogenetic protein 1	10/10
Gga.2933.1.S1_at	N-acetylglucosaminyltransferase VI	10/10
GgaAffx.20398.1.S1_s_at	phospholipase C-like 3	10/10

a: mismatching probes pairs in the total probes (10 pairs) that represent certain genes.

Table 5

Differentially expressed genes by microarray analysis

Probe set ID	Fold Change (fat/lean)	T-test P-value	SAM q-value	Chr. Location	GenBank ID	Gene name

Lipid Metabolism
GgaAffx.24836.1.S1_at	2.5	0.001	0.27	chr1: 100587339–100699482	XM_416725	propionyl-Coenzyme A-carboxylase
GgaAffx.22084.1.S1_at	1.8	0	0.27	chr11: 59355–69450	No record	lysophospholipase 3
Gga.150.1.S1_at	4.2	0.003	0.279	chr1: 167849591–167950628	NM_204252	fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)
GgaAffx.8095.1.S1_at	1.6	0.006	0.324	chr1: 52216531–52245657	XM_416329	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits
Gga.879.1.S1_at	-6.7	0.001	0.27	chr11: 16001674–16006281	NM_205526	N-acetyltransferase
Gga.19791.1.S1_s_at	1.9	0.003	0.279	chr2: 128797196–128808892	XM_418378	low density lipoprotein-related protein 12
GgaAffx.9942.1.S1_at	2.2	0.001	0.27	chr4: 81245396–81273837	XM_420814	acyl-CoA oxidase
GgaAffx.20938.1.S1_at	1.3	0.007	0.329	chr5: 15830450–15831289	NM_001031187	pyruvate dehydrogenase complex, component X similar to glycerol-3-phosphate dehydrogenase 2;
GgaAffx.23939.1.S1_s_at	7.5	0.005	0.301	chr7: 36699654–36750512	XM_422168	glycerol phosphate dehydrogenase 1, mitochondrial; FAD-linked glycerol-3-phosphate dehydrogenase
Gga.17037.1.S1_s_at	1.6	0.005	0.308	chrZ: 15403025–15434404	NM_001031422	phosphatidylinositol-4-phosphate 5-kinase, type I, beta
GgaAffx.5721.1.S1_at	2.1	0.001	0.27	chr3: 9206064–9214413	NM_001031039	lysocardiolipin acyltransferase
Energy Metabolism
Gga.11825.1.S1_at	3.2	0.003	0.274	chr1: 109208120–109232230	XM_416788	glycerol kinase
Gga.9828.1.S1_a_at	-3.2	0	0.27	chr1: 79394222–79396236	XM_416612	thioredoxin-like 4B
GgaAffx.4389.1.S1_at	-1.6	0.004	0.284	chr10: 17276047–17283495	XM_425083	5-oxoprolyl-peptidase
GgaAffx.2243.2.S1_at	2.3	0.002	0.27	chr26: 3685185–3702282	XM_418055	ATPase, Ca++ transporting, plasma membrane 4
Gga.19534.1.S1_at	8.3	0.002	0.27	chr9: 21559961–21563214	">XM_422814">	beta 1,3-galactosyltransferase, polypeptide 3
Tumorigenesis
Gga.6519.1.S1_s_at	-2.2	0.005	0.303	chr1: 21687403–21784133	XM_416014	suppression of tumorigenicity 7
Gga.15871.1.S1_at	-1.6	0.006	0.323	chr19: 8852117–8853712	CR387378	Tumor necrosis factor, alpha-induced protein 1
Gga.12058.1.S1_at	2.1	0.003	0.279	chr2: 135144222–135145306	XM_418407	similar to cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome
GgaAffx.22987.1.S1_at	-1.6	0.002	0.27	chr5: 26523325–26529591	XM_421205	thrombospondin 1
Gga.654.1.S2_at	1.8	0.001	0.27	chr6: 4237546–4314610	NM_205190	ret proto-oncogene
Signal Transduction
GgaAffx.3663.1.S1_at	-5.3	0.003	0.278	chr14: 8517712–8520620	XM_414857	similar to CASK interacting protein 1
Gga.12193.1.S1_a_at	9.0	0.007	0.324	chr2: 47562155–47581032	XM_418851	G-substrate
Gga.9510.1.S1_at	1.9	0.007	0.329	chr22:537865–569787	NM_001030886	protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), alpha isoform
Gga.1761.2.S1_at	13.8	0.002	0.27	chr3:107742849–107744353	XM_420066	similar to G-protein coupled receptor 116
GgaAffx.4775.1.S1_s_at	4.0	0.002	0.27	chr4:11707299–11760821	XM_420292	similar to receptor tyrosine kinase flk-1/VEGFR-2
Gga.807.1.S1_at	1.9	0.007	0.324	chr4:65686004–65686340	NM_001004368	kinase insert domain receptor (a type III receptor tyrosine kinase) (KDR)
Gga.12481.1.S1_s_at	1.9	0.007	0.327	chr7:27843665–27860405	NM_001012920	protein tyrosine phosphatase-like (proline instead of catalytic arginine), member b
Gga.6653.1.S1_at	-1.7	0.004	0.281	chr11:17426083–17429654	NM_001030576	hepatic nuclear factor 4beta similar to suppressor of cytokine signaling 7; SH2
GgaAffx.8729.1.S1_s_at	-10.0	0	0.27	chrUn:137141542–137146475	XM_423895	domain containing SOCS box protein SOCS7; Nck, Ash and phospholipase C binding protein similar to prostaglandin E receptor 3; Rat kidney
GgaAffx.7207.1.S1_at	5.7	0.002	0.27	chr8:29278163–29285596	XM_426672	prostaglandin EP3 receptor (alternative splicing results in two different receptors EP3a and EP3b);
Gga.10737.1.S1_s_at	1.7	0.005	0.305	chr7:2212065–2223469	XM_421856	similar to Nck-associated protein 1 (NAP 1) (p125Nap1) (Membrane-associated protein HEM- 2)
GgaAffx.8719.1.S1_at	7.2	0.002	0.27	chr4:64869759–64912904	XM_420693	similar to regulator protein p122-RhoGAP – rat
Gga.12408.3.S1_a_at	2.7	0.005	0.305	chr5:41375030–41383659	NM_204357	ataxin 3
Gga.323.1.S1_at	3.6	0.001	0.27	chrUn:147862083–147882739	NM_204801	tetraspanin 18
Immunity
Gga.13806.1.S1_at	-4.8	0.004	0.293	chr7:7186627–7189336	NM_204240	adenosine deaminase, RNA-specific, B1 (RED1 homolog rat)
Gga.18504.1.S1_at	6.9	0.003	0.278	chr5:5440836–5460278	CR390783	parvin, alpha
Gga.698.1.S1_at	1.6	0.004	0.293	chr6:14652488–14704778	NM_205441	vinculin
Gga.11155.1.S1_s_at	1.8	0.001	0.27	chr4:15341234–15354773	XM_420331	stromal antigen 2
Others
Gga.11258.1.S1_at	1.7	0.001	0.27	chr1:170378838–170513289	XM_417140	EF-hand domain family, member A1
Gga.15085.2.S1_s_at	6.6	0.001	0.27	chr1:172635432–172645292	XM_417167	CWF19-like 2, cell cycle control (S. pombe)
GgaAffx.5969.1.S1_at	6.2	0.002	0.27	chr1:24071401–24234367	XM_416024	similar to dedicator of cytokinesis 4
GgaAffx.12338.1.S1_s_at	3.9	0.001	0.27	chr15:7114454–7122253	NM_001030665	tuftelin interacting protein 11
GgaAffx.25724.1.S1_s_at	7.4	0.002	0.27	chr18:5638526–5691321	XM_415648	similar to Stxbp4 protein
GgaAffx.6849.1.S1_at	4.0	0.004	0.285	chr3:34026676–34050970	XM_419554	similar to endoplasmic reticulum oxidoreductin 1- Lbeta
GgaAffx.22370.3.S1_s_at	4.3	0	0.27	chr3:1260579–1276286	XM_420116	similar to chromosome 17 open reading frame 28; downregulated in multiple cancer 1
GgaAffx.6334.2.S1_at	3.9	0.004	0.293	chr4:33725503–33732138	XM_420444	SH3 domain protein D19
GgaAffx.22790.1.S1_s_at	6.1	0.003	0.279	chr6:26875122–27047419	XM_421771	similar to actin-binding LIM protein 1 medium isoform
GgaAffx.26704.1.S1_at	-5.2	0.001	0.27	chr8:14622890–14638649	XM_422345	similar to abhydrolase domain containing 7
Gga.16560.1.S1_at	3.3	0.003	0.279	chrE26C13:1961–7813	XM_422853	myeloid cell leukemia sequence 1 (BCL2-related)
Gga.16020.1.S1_at	2.2	0	0.27	chrUn:92422001–92432256	NM_001031613	similar to Death-associated protein kinase 1

Table 6

Primer pairs used to analyze gene expression by quantitative RT-PCR, and size of product

Gene	Forward primer^a	Reverse primer^a	Size

PCC	AGGGAAAGGTCGTGGCG	CCACTGCCAAGGACACTAGG	137 bp
PBP2	GAGTAAAGTCCGAGAACGAATG	AAATCCAGTAGTGGGACAAAGG	185 bp
TNFAIP1	TTCACTCTTAGAAATGCTGGTG	CTAAGTTAGTGGCAAAGCTGG	169 bp
FLT1	CTCTTTGGCATGAAAGGTGTC	CGTAGGTGTATCTTCGCTTGG	124 bp
G3PD	CTCCCATCCCATACCGACAG	GGCATATCGACTGCGTGTCC	167 bp
LRP12	GGAGTGTCAACGGCTTGTGG	ATCGGCGTGATCCCTGAACA	184 bp
PER	GGATCATGTGCGTCCTGTC	GGAGCAGCAGATAAACCCAC	210 bp
ST7	GTTCTATGTTGCCTTGACAGG	AAGTGGCTCACCGAGACCT	120 bp
ERO1	TTCAAGCCTCGATCTGTCTA	TCAAGAAGATAATTGGCACAC	182 bp
ATXN3	AAAGGTGACCTGCCAGAC	TTGCTTGGTCCACATCAC	142 bp
PARVA	GTGTACTTAGTCCTGCTAATGGG	TCTGGTCTGGGCTTTGGTT	161 bp
CWF19	ATCCCAGGGAAGTCTCGC	CTTTAGGCTCCTGTGGTTCAG	127 bp
Stxbp4	CCAAGATTTGAGAAAGAGGGTT	TCACTTAGAACAGCCGAGGAA	162 bp
ACO	GCTGTGCTCTATCAAGGTGGC	ACAAGGGCAACTGCGTCATC	110 bp
SOCS7	CATCCCAAGTTTGAAGACCG	CATTGCTGAACCTGGAGACG	163 bp
GAPDH	AGAACATCATCCCAGCGT	AGCCTTCACTACCCTCTTG	184 bp

a,: Sequences of oligonucleotides are indicated from 5' to 3' end

Table 7

Comparison of microarray and real-time RT-PCR analyses

Gene	Microarray^a	Real-time RT-PCR

	Fold change(F/L)^b	Fold change(F/L)^b	Student T-test^c(p-value)

PCC	2.5	2.45	0.0312*
ATXN3	2.7	4.47	0.0241*
PER	5.67	8.08	0.007**
ERO1	3.94	3.66	0.0308*
FLT1	4.21	4.46	0.0455*
CWF19	6.56	1.95	0.03*
PBP2	6.95	5.75	0.0521
PARVA	6.90	3	0.0221*
G3PD	7.46	2.32	0.0154*
Stxbp4	7.35	2.8	0.0031**
LRP12	1.82	8.83	0.0404*
ACO	2.19	2.76	0.2912
ST7	-2.1	-2.07	0.0042**
SOCS7	-10.0	-1.41	0.2117
TNFAIP1	-1.6	1.72	0.0086**

^a: Microarray F/L fold changes are taken from Table 5.
^b: Fold changes (F/L: mean of fat sample values on mean of lean sample values).
^c:Student's t-test p-values, *p

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Tables - Profiling of chicken adipose tissue gene expression by genome array

Tables
- Profiling of chicken adipose tissue gene expression by genome array