Table 2. Upregulated genes expressed at least five-fold higher in USPC compared with NEC.

Probe set	Gene symbol	SAM	P of WRS	Ratio USPC/NEC	Title
1713_s_at	CDKN2A a	10.592	0.0027	101.9077377	‘Cyclin-dependent kinase inhibitor 2A (melanoma, p16)’
36288_at	KRTHB1	4.573	0.0027	77.3983986	‘Keratin, hair, basic, 1’
33272_at	SAA1	3.778	0.0063	45.74937337	Serum amyloid A1
41294_at	KRT7	7.173	0.0027	41.46788873	Keratin 7
32154_at	TFAP2A	7.637	0.0027	32.47929396	Transcription factor AP-2 alpha
31610_at	MAP17	3.621	0.0093	30.28302802	Membrane-associated protein 17
408_at	—	4.070	0.0063	30.14111158	—
32821_at	LCN2	5.126	0.0027	27.69975608	Lipocalin 2 (oncogene 24p3)
35174_i_at	EEF1A2	2.840	0.0278	26.80482891	Elongation factor 1 alpha 2
38551_at	L1CAM	3.115	0.0196	25.60938089	‘L1 cell adhesion molecule
38249_at	VGLL1	5.274	0.0027	24.69495091	Vestigial like 1 (Drosophila)
35879_at	GAL	5.594	0.0027	23.48953559	Galanin
36838_at	KLK10	3.455	0.0136	23.17518549	Kallikrein 10
38299_at	IL6	3.630	0.0041	19.05873079	‘Interleukin 6 (interferon, beta 2)’
38051_at	MAL	4.878	0.0041	17.51555106	‘mal, T-cell differentiation protein’
41469_at	PI3	2.854	0.0063	16.90464558	‘Protease inhibitor 3, skin-derived (SKALP)’
40412_at	PTTG1	5.218	0.0027	16.61222352	Pituitary tumour-transforming 1
1886_at	WNT7A	3.544	0.0196	16.11519778	‘Wingless-type MMTV integration site family, member 7A’
33128_s_at	CST6	4.222	0.0136	15.97856318	Cystatin E/M
38414_at	CDC20	7.317	0.0027	15.64601435	CDC20 cell division cycle 20 homolog (S. cerevisiae)
34012_at	KRTHA4	2.411	0.0278	15.37247475	‘Keratin, hair, acidic, 4’
37554_at	KLK6	3.785	0.0093	15.23781352	‘Kallikrein 6 (neurosin, zyme)’
1802_s_at	ERBB2	2.566	0.0136	14.52012028	‘v-erb-b2’
41060_at	CCNE1	6.092	0.0027	14.16647068	Cyclin E1
36837_at	KIF2C	6.130	0.0027	14.1328483	Kinesin family member 2C
34213_at	KIBRA	5.301	0.0027	13.27228177	KIBRA protein
1651_at	UBE2C	5.554	0.0027	12.87617243	Ubiquitin-conjugating enzyme E2C
35276_at	CLDN4	6.381	0.0027	12.74825421	Claudin 4
36990_at	UCHL1	4.623	0.0027	12.30505908	Ubiquitin carboxyl-terminal esterase L1
35977_at	DKK1	4.495	0.0041	12.25382636	Dickkopf homolog 1 (Xenopus laevis)
36113_s_at	TNNT1	4.072	0.0027	11.93824813	‘Troponin T1, skeletal, slow’
2011_s_at	BIK	3.451	0.0063	11.66959681	BCL2-interacting killer (apoptosis-inducing)
543_g_at	CRABP1	3.193	0.0093	11.55494382	Cellular retinoic acid binding protein 1
34852_g_at	STK6	6.225	0.0027	11.51812047	Serine/threonine kinase 6
33483_at	NMU	4.094	0.0027	11.42057993	Neuromedin U
39109_at	TPX2	6.162	0.0027	11.29208457	‘TPX2, microtubule-associated protein homologue’
37018_at	HIST1H1C	2.270	0.0278	10.74270622	‘Histone 1, H1c’
1165_at	IL18	3.221	0.0041	10.65596528	Interleukin 18 (interferon-gamma-inducing factor)
36477_at	TNNI3	2.867	0.0136	10.61101382	‘Troponin I, cardiac’
572_at	TTK	3.720	0.0093	9.723902052	TTK protein kinase
31542_at	FLG	2.622	0.0196	9.600831601	Filaggrin
35937_at	MICB	4.238	0.0093	9.460109582	MHC class I polypeptide-related sequence B
36155_at	SPOCK2	2.278	0.0278	9.216570003	‘Sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 2’
32186_at	SLC7A5	4.149	0.0063	9.121679665	‘Solute carrier family 7 (cationic amino-acid transporter, y+ system), member 5’
35766_at	KRT18	5.933	0.0027	9.01220054	Keratin 18
35822_at	BF	3.267	0.0063	8.952514469	‘B-factor, properdin’
35714_at	PDXK	6.550	0.0027	8.898191704	‘Pyridoxal (pyridoxine, vitamin B6) kinase’
1369_s_at	—	2.679	0.0196	8.773380878	—
40079_at	RAI3	4.516	0.0063	8.626843209	Retinoic acid induced 3
37168_at	LAMP3	2.838	0.0136	8.616807346	Lysosomal-associated membrane protein 3
39704_s_at	HMGA1	5.322	0.0027	8.597894471	High-mobility group AT-hook 1
1887_g_at	WNT7A	3.003	0.0196	8.491813649	‘Wingless-type MMTV integration site family, member 7A’
36929_at	LAMB3	5.770	0.0027	8.354149098	‘Laminin, beta 3’
527_at	CENPA	6.126	0.0027	8.32992789	‘Centromere protein A, 17 kDa’
41081_at	BUB1	4.883	0.0027	8.213759056	BUB1 budding uninhibited by benzimidazoles 1 homologue
885_g_at	ITGA3	4.447	0.0027	8.20660555	‘Integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)’
2021_s_at	CCNE1	4.399	0.0041	8.199388463	Cyclin E1
33904_at	CLDN3	3.296	0.0136	8.020010794	Claudin 3
33730_at	RAI3	4.648	0.0041	7.923899439	Retinoic acid induced 3
34736_at	CCNB1	5.078	0.0063	7.896644626	Cyclin B1
757_at	ANXA2	3.514	0.0063	7.870466864	Annexin A2
910_at	TK1	3.934	0.0093	7.869091533	‘Thymidine kinase 1, soluble’
34851_at	STK6	4.491	0.0041	7.764803777	Serine/threonine kinase 6
34703_f_at	—	2.275	0.0278	7.710260816	—
34715_at	FOXM1	5.318	0.0027	7.659023602	Forkhead box M1
38971_r_at	TNIP1	6.800	0.0027	7.595036872	TNFAIP3 interacting protein 1
32263_at	CCNB2	4.246	0.0063	7.578513543	Cyclin B2
1680_at	GRB7	4.013	0.0027	7.471384928	Growth factor receptor-bound protein 7
38247_at	F2RL1	3.185	0.0093	7.432476326	Coagulation factor II (thrombin) receptor-like 1
160025_at	TGFA	6.088	0.0027	7.355344272	‘Transforming growth factor, alpha’
1945_at	CCNB1	5.298	0.0041	7.291039832	Cyclin B1
31792_at	ANXA3	4.873	0.0041	7.266892828	Annexin A3
182_at	ITPR3	5.432	0.0027	7.172450367	‘Inositol 1,4,5-triphosphate receptor, type 3’
1117_at	CDA	2.937	0.0093	7.114518646	Cytidine deaminase
902_at	EPHB2	5.186	0.0027	7.065363569	EphB2
634_at	PRSS8	5.216	0.0041	7.001894703	‘Protease, serine, 8 (prostasin)’
41169_at	PLAUR	3.982	0.0063	7.00139089	‘Plasminogen activator, urokinase receptor’
33203_s_at	FOXD1	3.464	0.0093	6.989749222	Forkhead box D1
40095_at	CA2	4.285	0.0027	6.946396937	Carbonic anhydrase II
38940_at	AD024	5.065	0.0041	6.928406028	AD024 protein
34348_at	SPINT2	6.263	0.0027	6.877224695	‘Serine protease inhibitor, Kunitz type, 2’
33933_at	WFDC2	3.344	0.0136	6.820073691	WAP four-disulphide core domain 2
35281_at	LAMC2	3.347	0.0093	6.7580474	‘Laminin, gamma 2’
349_g_at	KIFC1	5.275	0.0041	6.700913018	Kinesin family member C1
33218_at	ERBB2	2.710	0.0027	6.615105998	‘v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)’
38881_i_at	TRIM16	3.001	0.0196	6.506893575	Tripartite motif-containing 16
1536_at	CDC6	4.666	0.0041	6.463305623	CDC6 cell division cycle 6 homolog (S. cerevisiae)
38482_at	CLDN7	4.931	0.0041	6.409117877	Claudin 7
40697_at	CCNA2	3.396	0.0093	6.40768505	Cyclin A2
41688_at	TM4SF11	4.390	0.0027	6.366861533	Transmembrane 4 superfamily member 11 (plasmolipin)
38158_at	ESPL1	6.007	0.0027	6.225688779	Extra spindle poles like 1 (S. cerevisiae)
38474_at	CBS	3.380	0.0093	6.212078913	Cystathionine-beta-synthase
36483_at	GALNT3	3.890	0.0041	6.181109111	UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3 (GalNAc-T3)
35372_r_at	IL8	2.360	0.0278	6.133149591	Interleukin 8
41585_at	KIAA0746	4.436	0.0027	6.092207586	KIAA0746 protein
36832_at	B3GNT3	5.457	0.0027	5.941291793	‘UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 3’
1107_s_at	G1P2	3.938	0.0063	5.923287019	‘Interferon, alpha-inducible protein (clone IFI-15K)’
35207_at	SCNN1A	3.076	0.0136	5.920739634	‘Sodium channel, nonvoltage-gated 1 alpha’
36863_at	HMMR	2.830	0.0196	5.905038013	Hyaluronan-mediated motility receptor (RHAMM)
38631_at	TNFAIP2	4.924	0.0027	5.897745642	‘Tumour necrosis factor, alpha-induced protein 2’
36813_at	TRIP13	5.666	0.0027	5.870351247	Thyroid hormone receptor interactor 13
41048_at	PMAIP1	3.490	0.0062	5.853172336	Phorbol-12-myristate-13-acetate-induced protein 1
2084_s_at	ETV4	3.743	0.0093	5.798002338	‘ets variant gene 4 (E1A enhancer binding protein, E1AF)’
33245_at	MAPK13	3.775	0.0136	5.766618762	Mitogen-activated protein kinase 13
37347_at	CKS1B	5.543	0.0027	5.762817533	CDC28 protein kinase regulatory subunit 1B
34282_at	NFE2L3	2.668	0.0136	5.734907375	Nuclear factor (erythroid-derived 2)-like 3
330_s_at	—	4.026	0.0041	5.726752495	—
41732_at	na	6.920	0.0027	5.706487141	Similar to My016 protein
1516_g_at	—	6.726	0.0027	5.63870137	—
904_s_at	TOP2A	3.419	0.0063	5.634251452	Topoisomerase (DNA) II alpha 170 kDa
36041_at	EXO1	4.971	0.0027	5.59235892	Exonuclease 1
33143_s_at	SLC16A3	4.007	0.0063	5.56591457	‘Solute carrier family 16 (monocarboxylic acid transporters), member 3’
37228_at	PLK	4.501	0.0041	5.564532365	Polo-like kinase (Drosophila)
1854_at	MYBL2	4.117	0.0063	5.54317592	v-myb myeloblastosis viral oncogene homolog (avian)-like 2
40407_at	KPNA2	4.189	0.0041	5.51635645	‘Karyopherin alpha 2 (RAG cohort 1, importin alpha 1)’
33282_at	LAD1	3.904	0.0063	5.509367036	Ladinin 1
40145_at	TOP2A	3.307	0.0093	5.48127065	Topoisomerase (DNA) II alpha 170 kDa
1100_at	IRAK1	5.530	0.0027	5.470162749	Interleukin-1 receptor-associated kinase 1
37883_i_at	AF038169	3.160	0.0027	5.460495655	Hypothetical protein AF038169
37343_at	ITPR3	5.258	0.0027	5.449013729	‘Inositol 1,4,5-triphosphate receptor, type 3’
31598_s_at	GALE	4.647	0.0027	5.442955253	‘Galactose-4-epimerase, UDP-’
889_at	ITGB8	2.744	0.0093	5.370592815	‘Integrin, beta 8’
37558_at	IMP-3	3.123	0.0093	5.364127468	IGF-II mRNA-binding protein 3
32715_at	VAMP8	5.686	0.0027	5.352873419	Vesicle-associated membrane protein 8 (endobrevin)
36312_at	SERPINB8	3.611	0.0027	5.327343554	‘Serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 8’
37210_at	INA	3.551	0.0063	5.307526088	‘Internexin neuronal intermediate filament protein, alpha’
35699_at	BUB1B	3.665	0.0196	5.279075308	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)
32787_at	ERBB3	2.658	0.0041	5.247404657	v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian)
32275_at	SLPI	3.726	0.0041	5.221163981	Secretory leukocyte protease inhibitor (antileukoproteinase)
893_at	E2-EPF	3.775	0.0063	5.196412396	Ubiquitin carrier protein
41583_at	FEN1	5.481	0.0027	5.196005796	Flap structure-specific endonuclease 1
41781_at	PPFIA1	4.113	0.0027	5.194931774	‘Protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1’
40726_at	KIF11	2.941	0.0093	5.1806793	Kinesin family member 11
41400_at	TK1	4.246	0.0093	5.167172588	‘Thymidine kinase 1, soluble’
41409_at	C1orf38	3.109	0.0063	5.100239097	Chromosome 1 open reading frame 38
40425_at	EFNA1	2.738	0.0196	5.067718102	Ephrin-A1
32081_at	CIT	6.162	0.0027	5.043567722	‘Citron (rho-interacting, serine/threonine kinase 21)’
1108_s_at	EPHA1	4.864	0.0027	5.040980858	EphA1
33338_at	STAT1	3.275	0.0063	5.029498048	‘Signal transducer and activator of transcription 1, 91 kDa’

^aGenes selected for further analysis are identified with bold letters.