Supplementary Table 2
Genes downregulated in Pancreatic Endocrine Neoplasms
probe set	gene	fold change	lower bound of FC	upper bound of FC	difference of means	t statistic	P value
201951_at	activated leucocyte cell adhesion molecule	-3.244657	-1.52939	-5.80867	-116.64	-2.21151	0.051429
208074_s_at	adaptor-related protein complex 2, sigma 1 subunit	-3.652972	-1.38638	-11.7547	-169.692	-2.00687	0.072552
209122_at	adipose differentiation-related protein	-3.473924	-1.56589	-6.6298	-181.519	-2.20054	0.052393
220525_s_at	ancient ubiquitous protein 1	-3.541587	-1.32382	-7.77042	-125.469	-1.91774	0.084123
201302_at	annexin A4	-3.443139	-1.7166	-7.28188	-321.22	-2.52949	0.029897
201028_s_at	antigen identified by monoclonal antibodies 12E7, F21 and O13	-3.347842	-1.78412	-6.41574	-384.037	-2.70069	0.022287
200844_s_at	anti-oxidant protein 2 (non-selenium glutathione peroxidase, acidic calcium-independent phospholipase A2)	-4.182166	-2.78556	-7.30835	-389.415	-5.88034	0.000155
202655_at	arginine-rich, mutated in early stage tumors	-3.793247	-1.40973	-13.3462	-845.151	-2.01453	0.071631
200729_s_at	ARP2 actin-related protein 2 homolog (yeast)	-3.001098	-1.44248	-7.66733	-197.278	-2.29297	0.044787
214594_x_at	ATPase, Class I, type 8B, member 1	-4.354071	-1.45417	-8.15024	-60.9219	-1.91434	0.084596
200954_at	ATPase, H+ transporting, lysosomal (vacuolar proton pump) 16kD	-4.806673	-2.1839	-11.5377	-219.232	-2.61111	0.025991
212041_at	ATPase, H+ transporting, lysosomal (vacuolar proton pump), member D	-4.118721	-2.54708	-8.55452	-267.21	-4.99601	0.000541
213104_at	BAI1-associated protein 3	-3.697666	-2.07022	-6.4185	-58.8663	-2.9745	0.013938
204872_at	BCE-1 protein	-3.600075	-1.23424	-7.01822	-149.928	-1.81858	0.099006
219072_at	B-cell CLL/lymphoma 7C	-3.312449	-1.96227	-5.78838	-174.052	-3.20443	0.009421
217911_s_at	BCL2-associated athanogene 3	-3.620577	-1.72326	-6.1255	-217.483	-2.32157	0.042659
221972_s_at	calcium binding protein Cab45 precursor	-4.266386	-1.63659	-9.64375	-122.625	-2.10622	0.061431
202122_s_at	cargo selection protein (mannose 6 phosphate receptor binding protein)	-3.004518	-1.76866	-5.39827	-147.154	-3.03076	0.012661
207980_s_at	Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2	-3.850563	-1.31634	-9.07095	-120.246	-1.87809	0.089806
209953_s_at	CDC37 cell division cycle 37 homolog (S. cerevisiae)	-4.924349	-1.37753	-11.107	-90.1326	-1.8338	0.096574
218333_at	CGI-101 protein	-3.372532	-1.93701	-9.35074	-194.484	-3.99715	0.00253
200812_at	chaperonin containing TCP1, subunit 7 (eta)	-3.983956	-2.20027	-7.92512	-204.249	-3.19286	0.009607
213038_at	Consensus includes gb:AL031602 /DEF=Human DNA sequence from clone RP5-1174N9 on chromosome 1p34.1-35.3. Contains the gene for a novel protein with IBR domain, a (pseudo?) gene for a novel protein similar to MT1E (metallothionein 1E (functional)), ESTs, S	-3.389319	-1.94256	-6.53403	-124.682	-3.16949	0.009996
216348_at	Consensus includes gb:AL049693 /DEF=Human DNA sequence from clone RP4-753D5 on chromosome 6p12.1-12.3. Contains the 3 end of the TFAP2B gene for transcription factor AP-2 beta (activating enhancer-binding protein 2 beta), the gene for a novel protein sim	-4.059182	-2.11544	-8.23357	-160.366	-2.89118	0.016075
216858_x_at	Consensus includes gb:AL080112.1 /DEF=Homo sapiens mRNA; cDNA DKFZp586H0722 (from clone DKFZp586H0722). /FEA=mRNA /DB_XREF=gi:5262539 /UG=Hs.332731 Homo sapiens mRNA; cDNA DKFZp586H0722 (from clone DKFZp586H0722)	-3.487867	-1.34283	-7.70233	-82.7472	-1.94702	0.080143
216570_x_at	Consensus includes gb:AL096829 /DEF=Human DNA sequence from clone RP4-595K12 on chromosome 1p31.2-31.3 Contains a pseudogene similar to 60S RPL29 (ribosomal protein L29 (cell surface heparin binding protein HIP)), a chromosome 1 specific mRNA (KIAA0499),	-3.306955	-1.74847	-5.92929	-304.175	-2.59161	0.026876
217019_at	Consensus includes gb:AL137162 /DEF=Human DNA sequence from clone RP5-843L14 on chromosome 20. Contains ESTs, STSs and GSSs. Contains a novel gene and the 5 part of a gene for a novel protein similar to X-linked ribosomal protein 4 (RPS4X) /FEA=CDS /DB_X	-3.119308	-1.6086	-5.80693	-145.509	-2.4465	0.034463
213166_x_at	Consensus includes gb:BG332462 /FEA=EST /DB_XREF=gi:13138900 /DB_XREF=est:602432837F1 /CLONE=IMAGE:4550505 /UG=Hs.3343 phosphoglycerate dehydrogenase	-3.80259	-2.54941	-6.17316	-239.873	-4.95375	0.000575
217466_x_at	Consensus includes gb:L48784 /DEF=050 Homo sapiens cDNA /FEA=mRNA /DB_XREF=gi:1066715 /UG=Hs.182426 ribosomal protein S2	-4.067795	-1.97064	-6.59782	-311.147	-2.44702	0.034433
217125_at	Consensus includes gb:X04802 /DEF=Homo sapiens UBBP2 pseudogene for ubiquitin UBB /FEA=CDS /DB_XREF=gi:37582 /UG=Hs.247890 Homo sapiens UBBP2 pseudogene for ubiquitin UBB	-3.377313	-1.68	-8.88154	-138.257	-2.62208	0.025507
217347_at	Consensus includes gb:Z82202 /DEF=Human DNA sequence from clone RP1-34P24 on chromosome 22 Contains a pseudogene similar to ribosomal protein L35, ESTs, STSs and GSSs /FEA=CDS /DB_XREF=gi:4107193 /UG=Hs.247778 Human DNA sequence from clone RP1-34P24 on c	-3.141567	-1.92603	-5.47719	-172.287	-3.40925	0.006667
202284_s_at	cyclin-dependent kinase inhibitor 1A (p21, Cip1)	-5.18934	-1.96565	-11.2862	-882.89	-2.20444	0.052049
208842_s_at	DKFZP434D156 protein	-4.250934	-2.20519	-7.98333	-481.199	-2.83981	0.017554
208843_s_at	DKFZP434D156 protein	-3.046378	-1.49415	-5.25943	-524.351	-2.22488	0.050277
208499_s_at	DnaJ (Hsp40) homolog, subfamily C, member 3	-3.692707	-1.67297	-7.44023	-66.804	-2.29076	0.044956
208675_s_at	dolichyl-diphosphooligosaccharide-protein glycosyltransferase	-3.539022	-1.44829	-6.62255	-538.647	-2.02912	0.069907
202596_at	endosulfine alpha	-3.46889	-1.85859	-7.87309	-392.139	-2.95515	0.014407
202017_at	epoxide hydrolase 1, microsomal (xenobiotic)	-4.116213	-1.32145	-8.38928	-462.8	-1.84753	0.094427
204540_at	eukaryotic translation elongation factor 1 alpha 2	-3.651788	-1.55338	-8.74594	-251.621	-2.183	0.053971
203113_s_at	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)	-3.968385	-1.39354	-7.04229	-552.161	-1.90427	0.086014
208625_s_at	eukaryotic translation initiation factor 4 gamma, 1	-5.807913	-1.55309	-12.9124	-135.077	-1.87312	0.090543
221539_at	eukaryotic translation initiation factor 4E binding protein 1	-7.023146	-2.01662	-36.8946	-189.181	-2.06107	0.066269
201637_s_at	fragile X mental retardation, autosomal homolog 1	-4.864059	-2.03166	-16.1997	-218.51	-2.48083	0.032497
218070_s_at	GDP-mannose pyrophosphorylase A	-3.137523	-1.71575	-5.83779	-135.556	-2.70259	0.022214
202354_s_at	general transcription factor IIF, polypeptide 1 (74kD subunit)	-4.159119	-1.33726	-8.13146	-56.3898	-1.85262	0.093642
202320_at	general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )	-4.405653	-2.59056	-10.3142	-120.816	-4.60002	0.00098
208336_s_at	glycoprotein, synaptic 2	-3.040582	-1.56536	-5.72788	-156.752	-2.41275	0.036511
210658_s_at	golgi associated, gamma adaptin ear containing, ARF binding protein 2	-7.370815	-1.90465	-16.2933	-122.774	-1.93329	0.081987
201618_x_at	GPAA1P anchor attachment protein 1 homolog (yeast)	-3.737648	-2.14889	-6.96175	-85.7023	-3.28874	0.008167
203725_at	growth arrest and DNA-damage-inducible, alpha	-3.301458	-1.82325	-7.43187	-226.142	-3.07146	0.011811
209304_x_at	growth arrest and DNA-damage-inducible, beta	-7.523645	-2.24133	-16.173	-996.865	-2.05871	0.06653
207574_s_at	growth arrest and DNA-damage-inducible, beta	-5.555667	-1.76692	-11.0809	-776.379	-1.99787	0.07365
205354_at	guanidinoacetate N-methyltransferase	-6.782362	-1.94164	-21.9704	-173.993	-2.01709	0.071326
214431_at	guanine monphosphate synthetase	-3.251824	-1.33783	-5.95099	-113.516	-1.95805	0.07869
214290_s_at	H2A histone family, member O	-4.231056	-2.16203	-9.83792	-365.456	-2.97208	0.013996
208577_at	H3 histone family, member C	-4.130141	-1.49012	-7.39311	-50.0879	-1.96231	0.078136
201841_s_at	heat shock 27kD protein 1	-3.13392	-1.34513	-7.83392	-423.593	-2.046	0.067962
211936_at	heat shock 70kD protein 5 (glucose-regulated protein, 78kD)	-4.591946	-2.11079	-9.71322	-1135.86	-2.54614	0.029056
211968_s_at	heat shock 90kD protein 1, alpha	-3.017178	-1.88112	-6.88603	-468.266	-4.69554	0.000847
204610_s_at	hepatitis delta antigen-interacting protein A	-3.843966	-1.88892	-8.96105	-94.0744	-2.66816	0.023567
200593_s_at	heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A)	-3.055614	-1.18873	-5.52395	-162.244	-1.82083	0.098644
200643_at	high density lipoprotein binding protein (vigilin)	-3.624865	-2.00016	-6.63228	-400.225	-2.93835	0.014827
206445_s_at	HMT1 hnRNP methyltransferase-like 2 (S. cerevisiae)	-3.464156	-1.22282	-7.51301	-186.909	-1.82711	0.097637
212300_at	hypothetical protein FLJ10547	-3.614592	-1.49331	-7.65719	-93.5157	-2.08817	0.063323
222155_s_at	hypothetical protein FLJ11856	-3.736553	-1.69586	-11.3349	-72.3312	-2.45403	0.034022
206551_x_at	hypothetical protein FLJ20059	-6.024055	-2.13617	-16.478	-239.716	-2.21983	0.050709
219143_s_at	hypothetical protein FLJ20374	-4.507103	-2.87185	-8.16386	-146.428	-4.9714	0.000561
218938_at	hypothetical protein MGC11279	-3.123989	-1.51827	-6.19728	-74.1169	-2.28873	0.045111
219051_x_at	hypothetical protein MGC2601	-3.154175	-1.2123	-6.55465	-121.558	-1.84641	0.094601
218714_at	hypothetical protein MGC3121	-3.426197	-2.08981	-8.13888	-140.101	-4.85936	0.000662
208906_at	hypothetical protein MGC4694	-3.495355	-1.43464	-9.56357	-249.974	-2.08886	0.06325
221767_x_at	hypothetical protein PRO2900	-3.308653	-1.21152	-7.20414	-1001.76	-1.83169	0.096907
203751_x_at	jun D proto-oncogene	-7.567467	-4.08266	-11.202	-96.7603	-3.11967	0.01088
214326_x_at	jun D proto-oncogene	-11.710101	-4.63556	-23.9062	-212.624	-2.58696	0.027091
212219_at	KIAA0077 protein	-7.723961	-2.29918	-22.5089	-220.814	-2.09722	0.062368
212396_s_at	KIAA0090 protein	-4.994057	-1.7836	-18.9392	-137.544	-2.16864	0.055297
212348_s_at	KIAA0601 protein	-3.524191	-1.28347	-7.54496	-118.008	-1.8775	0.089893
214055_x_at	KIAA1096 protein	-4.9195	-1.35721	-11.1071	-88.7698	-1.82257	0.098363
201932_at	MUF1 protein	-3.372874	-1.91714	-6.77005	-140.686	-3.16447	0.010082
215338_s_at	natural killer-tumor recognition sequence	-3.112709	-1.35276	-5.99892	-51.1929	-2.01636	0.071413
204862_s_at	non-metastatic cells 3, protein expressed in	-4.7595	-2.12391	-16.9478	-106.829	-2.71499	0.021747
210470_x_at	non-POU-domain-containing, octamer-binding	-4.83431	-1.67896	-13.8296	-218.524	-2.07131	0.065141
204880_at	O-6-methylguanine-DNA methyltransferase	-3.204863	-1.50214	-6.67616	-79.737	-2.23734	0.049226
208993_s_at	peptidyl-prolyl isomerase G (cyclophilin G)	-3.41294	-2.47939	-4.81375	-126.717	-5.39245	0.000305
216606_x_at	PHD finger protein 1	-4.34317	-2.13038	-22.2915	-138.605	-3.3996	0.006776
211048_s_at	protein disulfide isomerase related protein (calcium-binding protein, intestinal-related)	-3.033632	-1.7716	-6.62966	-395.256	-3.34738	0.007398
201602_s_at	protein phosphatase 1, regulatory (inhibitor) subunit 12A	-3.569646	-1.39794	-6.92169	-69.7505	-1.9748	0.076532
208932_at	protein phosphatase 4 (formerly X), catalytic subunit	-3.697384	-1.4912	-9.21227	-105.754	-2.09409	0.062697
208549_x_at	prothymosin a14	-3.705625	-1.57835	-6.8455	-300.719	-2.13476	0.05855
208734_x_at	RAB2, member RAS oncogene family	-3.06994	-1.62543	-5.64733	-124.395	-2.5163	0.030581
212099_at	ras homolog gene family, member B	-3.387049	-1.53164	-6.44962	-935.427	-2.18165	0.054095
216589_at	ribosomal protein L10	-3.00236	-1.86737	-4.88615	-60.0683	-3.27327	0.008384
200869_at	ribosomal protein L18a	-4.039458	-2.33554	-6.92869	-633.647	-3.27288	0.008389
200823_x_at	ribosomal protein L29	-3.103307	-1.86866	-5.26188	-623.221	-3.15627	0.010223
216588_at	ribosomal protein L7	-3.269592	-1.54402	-6.54544	-81.3176	-2.26674	0.046829
208646_at	ribosomal protein S14	-3.098469	-1.4697	-6.49459	-190.716	-2.23016	0.049829
216380_x_at	ribosomal protein S28	-3.742521	-1.95903	-8.452	-324.715	-2.92206	0.015247
217747_s_at	ribosomal protein S9	-4.011791	-2.61175	-6.87965	-796.992	-4.81196	0.000711
208319_s_at	RNA binding motif protein 3	-3.320747	-2.00259	-5.34947	-201.702	-3.17383	0.009923
203607_at	Sac domain-containing inositol phosphatase 2	-5.36051	-1.60912	-17.8716	-321.458	-1.96241	0.078124
201543_s_at	SAR1 protein	-3.18332	-1.71991	-5.85839	-160.437	-2.65582	0.024071
218206_x_at	SCAN domain-containing 1	-3.541316	-2.2966	-7.20558	-244.424	-6.15709	0.000107
207707_s_at	SEC13-like 1 (S. cerevisiae)	-3.694515	-1.4081	-10.2915	-360.703	-2.00927	0.072262
212411_at	similar to HYPOTHETICAL 34.0 KDA PROTEIN ZK795.3 IN CHROMOSOME IV	-3.205513	-1.79638	-5.68156	-174.86	-2.80899	0.018507
217957_at	similar to mouse Glt3 or D. malanogaster transcription factor IIB	-3.209636	-1.54874	-6.09163	-258.949	-2.28273	0.045574
201138_s_at	Sjogren syndrome antigen B (autoantigen La)	-4.237237	-1.40922	-7.9394	-199.791	-1.89381	0.087511
212085_at	solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 6	-3.648719	-2.20411	-6.70963	-488.847	-3.69893	0.004116
200991_s_at	sorting nexin 17	-3.914022	-1.29199	-10.6675	-125.454	-1.85956	0.092582
218216_x_at	SRp25 nuclear protein	-3.112831	-1.82768	-5.59828	-307.519	-3.07981	0.011645
213330_s_at	stress-induced-phosphoprotein 1 (Hsp70/Hsp90-organizing protein)	-3.45698	-1.61803	-6.15816	-156.453	-2.25837	0.0475
209367_at	syntaxin binding protein 2	-3.047857	-1.79075	-6.93107	-80.8934	-3.51972	0.005541
208700_s_at	transketolase (Wernicke-Korsakoff syndrome)	-3.881654	-1.50229	-8.02584	-211.333	-2.03435	0.069299
214314_s_at	translation initiation factor IF2	-3.666032	-1.6234	-6.92212	-91.2305	-2.20922	0.051629
200598_s_at	tumor rejection antigen (gp96) 1	-4.534208	-1.69662	-9.02091	-242.342	-2.08645	0.063506
204559_s_at	U6 snRNA-associated Sm-like protein LSm7	-4.227928	-1.57683	-9.15553	-233.267	-2.04923	0.067595
201593_s_at	uncharacterized hypothalamus protein HT010	-10.591637	-2.69863	-42.2316	-297.367	-2.05434	0.06702
208649_s_at	valosin-containing protein	-3.020215	-1.74342	-6.96718	-206.775	-3.31469	0.007817
204175_at	zinc finger protein	-4.091999	-2.23897	-9.28052	-175.54	-3.37431	0.00707
217741_s_at	zinc finger protein 216	-3.164064	-1.20226	-6.04909	-191.61	-1.82796	0.097501