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Home , KIAA0515, PAS domain, RAB11B, Tyrosinase

Supplementary Table 1: Significantly upregulated in the “malignant” cluster of PNETs (p<0.05)

Fold change (WDEC/WDET) FEV 11.61 adenylate cyclase 2 (brain) 4.47 nuclear subfamily 4, group A, member 2 4.45 growth arrest and DNA-damage-inducible, beta 3.28 plexin B1 3.10 neuronal PAS domain protein 2 2.92 caldesmon 1 2.81 drebrin 1 2.43 hypothetical protein BC013764 2.41 TGFB-induced factor (TALE family ) 2.26 Homo sapiens cDNA FLJ12843 fis, clone NT2RP2003293, mRNA sequence 2.17 nuclear prelamin A recognition factor 2.15 chromobox homolog 4 (Pc class homolog, Drosophila) 2.14 RuvB (E coli homolog)-like 1 [Homo sapiens], mRNA sequence 2.03 latent transforming growth factor beta binding protein 4 2.02 putative glialblastoma cell differentiation-related 1.92 hypothetical protein FLJ10298 1.92 protein phosphatase type IVA, member 1 1.90 ADP-ribosylation factor-like 4 1.88 NIMA (never in mitosis gene a)-related kinase 7 1.87 RAB11B, member RAS oncogene family 1.87 myelin 1 1.86 centaurin, beta 2 1.83 Homo sapiens cDNA FLJ38575 fis, clone HCHON2007046, mRNA sequence 1.83 SH3 domain binding -rich protein like 3 1.81 immunoglobulin heavy constant gamma 3 (G3m marker) 1.77 chromobox homolog 3 (HP1 gamma homolog, Drosophila) 1.74 basic transcription element binding protein 1 1.73 H1 histone family, member X 1.73 protein phosphatase 2A, regulatory subunit B' (PR 53) 1.73 Homo sapiens cDNA FLJ30096 fis, clone BNGH41000045, mRNA sequence 1.73 KIAA0397 gene product 1.71 OK/SW-CL.4 [Homo sapiens], mRNA sequence 1.69 high-mobility group 20B 1.69 phosphoserine phosphatase 1.68 Homo sapiens mRNA; cDNA DKFZp434B142 (from clone DKFZp434B142), mRNA sequence 1.67 nuclear mitotic apparatus protein 1 1.67 hypothetical protein 628 1.66 PRKC, apoptosis, WT1, regulator 1.64 E3 ubiquitin SMURF1 1.64 chromodomain protein, Y -like 1.63 hypothetical protein FLJ21839 1.62 hypothetical protein MGC2550 1.62

Suppl. Table 1 (continued)

Fold Change Gene (WDEC/WDET) DAZ associated protein 2 1.61 replication factor C (activator 1) 2, 40kDa 1.60 likely ortholog of mouse , delta 1 1.59 FUS interacting protein (- rich) 1 1.58 fetal Alzheimer antigen 1.58 hypothetical protein FLJ13910 1.58 Homo sapiens clone 23718 mRNA sequence 1.58 plectin 1, intermediate filament binding protein 500kDa 1.58 hypothetical protein MGC3260 1.58 inhibitor of growth family, member 4 1.57 -like enhancer of split 3 (E(sp1) homolog, Drosophila) 1.57 high mobility group nucleosomal binding domain 3 1.57 Homo sapiens full length insert cDNA clone YY61D04, mRNA sequence 1.57 nucleoporin 62kDa 1.56 phosphoribosyl pyrophosphate synthetase-associated protein 2 1.56 PRO0974 [Homo sapiens], mRNA sequence 1.56 small nuclear RNA activating complex, polypeptide 3, 50kDa 1.56 actin, gamma 1 1.55 supervillin 1.55 glucosamine (N-acetyl)-6-sulfatase (Sanfilippo disease IIID) 1.55 polypyrimidine tract binding protein 1 1.54 calcium binding protein Cab45 precursor 1.54 hypothetical protein FLJ20294 1.53 intersectin 1 (SH3 domain protein) 1.52 1.52 vacuolar protein sorting 41 (yeast) 1.51 Homo sapiens cDNA FLJ38058 fis, clone CTONG2014898, mRNA sequence 1.51 transmembrane 9 superfamily member 1 1.50

Supplementary Table 2: Significantly downregulated genes in the “malignant” cluster of PNETs (p<0.05)

Fold Change Gene ((WDEC/WDET) ATP-binding cassette, sub-family C (CFTR/MRP), member 8 0.29 SH3-domain GRB2-like endophilin B1 0.41 Rag D protein 0.42 protocadherin 17 0.42 glucokinase (hexokinase 4, maturity onset diabetes of the young 2) 0.43 neuropeptide Y 0.46 hypothetical protein FLJ20559 0.46 sortilin-related receptor, L(DLR class) A repeats-containing 0.46 Homo sapiens, clone IMAGE:4133122, mRNA, mRNA sequence 0.47 pentaxin-related gene, rapidly induced by IL-1 beta 0.47 AD037 protein 0.47 Consensus includes gb:AF059180 /DEF=Homo sapiens mutant beta-globin (HBB) gene, complete cds /FEA=mRNA /DB_XREF=gi:4837722 /UG=Hs.155376 hemoglobin, beta 0.48 Homo sapiens cDNA: FLJ21930 fis, clone HEP04301, highly similar to HSU90916 Human clone 23815 mRNA sequence 0.49 growth factor receptor-bound protein 10 0.49 tyrosinase-related protein 1 0.51 alpha-methylacyl-CoA racemase 0.53 inositol 1,4,5-triphosphate receptor, type 3 0.54 FN5 protein 0.55 Hr44 antigen 0.55 phosphodiesterase 1C, calmodulin-dependent 70kDa 0.55 hemoglobin, beta 0.56 hemoglobin, delta 0.56 glutamate receptor, metabotropic 1 0.56 Hemoglobin gamma-G [Homo sapiens], mRNA sequence 0.56 Alpha one globin [Homo sapiens], mRNA sequence 0.57 hemoglobin, gamma G 0.58 hemoglobin, alpha 1 0.59 carbonic anhydrase IV 0.59 Endomucin-1 [Homo sapiens], mRNA sequence 0.60 carboxypeptidase A4 0.60 Rho guanine nucleotide exchange factor (GEF) 10 0.60 ESTs, Moderately similar to hypothetical protein FLJ20489 [Homo sapiens] [H.sapiens] 0.60 ADP-ribosylation factor 4-like 0.63 hemoglobin, alpha 2 0.63 adrenergic, alpha-2A-, receptor 0.63 Consensus includes gb:V00489 /DEF=Human alpha-globin gene with flanks /FEA=mRNA /DB_XREF=gi:28548 /UG=Hs.272572 hemoglobin, alpha 2 0.64 membrane protein, palmitoylated 1, 55kDa 0.64 lipase, hormone-sensitive 0.65 neuromedin B 0.65 a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2 0.66 neurofibromin 2 (bilateral acoustic neuroma) 0.66

Supplementary Table 3: Significantly upregulated genes in GI carcinoids when compared to PNETs (p<0.05)

Fold Change GI- Gene carcinoids/PNET extracellular matrix protein 1 28.08 solute carrier family 18 (vesicular monoamine), member 1 25.32 lectin, galactoside-binding, soluble, 4 (galectin 4) 24.04 cytochrome P450, subfamily IIIA, polypeptide 7 23.91 epidermal growth factor receptor pathway 8 related protein 3 21.13 homeo box C6 20.79 forkhead box A1 14 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial) 12.53 glucosidase, beta, acid 3 (cytosolic) 12.04 immunoglobulin kappa constant 11.1 cadherin 17, LI cadherin (liver-intestine) 10.6 apolipoprotein A-I 10.21 neuropeptide Y receptor Y1 9.99 Papillary thyroid carcinoma-encoded protein, mRNA sequence 9.47 hypothetical protein BC013764 9.02 anterior gradient 2 homolog (Xenepus laevis) 8.81 hephaestin 8.67 flavin containing 5 8.67 cytochrome P450, subfamily IIIA (niphedipine ), polypeptide 4 8.52 neurogranin (protein kinase C substrate, RC3) 8.42 HRAS-like suppressor 7.68 apolipoprotein D 7.67 Consensus includes gb:BF195104 /FEA=EST /DB_XREF=gi:11081627 /DB_XREF=est:7n15a07.x1 /CLONE=IMAGE:3564565 /UG=Hs.56729 lymphocyte-specific protein 1 7.63 tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin) 7.6 serine (or ) proteinase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2 7.31 M6A 7.3 B-factor, properdin 7.14 IA 6.98 immunoglobulin heavy constant mu 6.67 interferon consensus sequence binding protein 1 6.39 responder (tazarotene induced) 3 6.38 cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 5 5.73 KIAA1054 protein 5.7 breast carcinoma amplified sequence 1 5.68 breast cancer anti-estrogen resistance 3 5.56 homeodomain only protein 5.56 T cell receptor beta 5.48 carboxylesterase 1 (monocyte/macrophage serine esterase 1) 5.41 KIAA0233 gene product 5.36 lymphocyte antigen 75 5.33 retinoic acid receptor responder (tazarotene induced) 1 5.3

Suppl. Table 3 (continued)

Fold Change GI- Gene carcinoids/PNET Kruppel-like factor 5 (intestinal) 5.23 dopa decarboxylase (aromatic L- decarboxylase) 5.13 FEV protein 5 coagulation factor V (proaccelerin, labile factor) 4.73 sodium channel, voltage-gated, type III, alpha polypeptide 4.65 hypothetical protein DKFZp434B0417 4.62 phospholipase A2, group X 4.59 heparan sulfate (glucosamine) 3-O-sulfotransferase 1 4.42 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N- acetylgalactosaminyltransferase 10 (GalNAc-T10) 4.4 Homo sapiens mRNA; cDNA DKFZp564N1116 (from clone DKFZp564N1116), mRNA sequence 4.34 Mst3 and SOK1-related kinase 4.33 KIAA0830 protein 4.3 protocadherin LKC 4.27 absent in 1 4.07 ESTs, Moderately similar to T00636 hypothetical protein F21856_2 - human [H.sapiens] 4.05 KIAA0703 gene product 3.96 SMA5 3.92 ribonuclease, RNase A family, 4 3.91 annexin A13 3.82 fibroblast growth factor 13 3.79 hypothetical protein MGC2376 3.78 chemokine-like factor 1 3.66 hypothetical protein MGC2742 3.65 ret proto-oncogene (multiple endocrine neoplasia and medullary thyroid carcinoma 1, Hirschsprung disease) 3.62 DKFZP586C1619 protein 3.58 fatty-acid-Coenzyme A ligase, long-chain 5 3.58 protein 36, C3H type-like 2 3.52 KIAA1013 protein 3.44 latexin protein 3.44 KIAA0648 protein 3.4 family member 13B 3.37 potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3 3.37 SMA3 3.35 hypothetical protein FLJ14639 3.31 S100 calcium binding protein A6 (calcyclin) 3.31 homolog of rat orphan transporter v7-3 3.29 hypothetical protein MGC4309 3.29 tumor necrosis factor, alpha-induced protein 3 3.28 inositol 1,4,5-triphosphate receptor, type 1 3.28 Homo sapiens, clone IMAGE:3659798, mRNA, mRNA sequence 3.26 Homo sapiens, clone IMAGE:3659798, mRNA, mRNA sequence 3.26 plexin C1 3.24 cytochrome P450, subfamily XXVIIA (steroid 27-hydroxylase, cerebrotendinous xanthomatosis), polypeptide 1 3.16 fibroblast growth factor receptor 3 (achondroplasia, thanatophoric dwarfism) 3.16 Suppl. Table 3 (continued)

Fold Change GI- Gene carcinoids/PNET myosin XVB, pseudogene 3.15 Usher syndrome 1C (autosomal recessive, severe) 3.14 Homo sapiens mRNA; cDNA DKFZp586F071 (from clone DKFZp586F071), mRNA sequence 3.14 proteasome (prosome, macropain) subunit, beta type, 9 (large multifunctional protease 2) 3.11 baculoviral IAP repeat-containing 1 3.09 caldesmon 1 3 thioredoxin interacting protein 2.96 matrilin 2 2.96 CUG triplet repeat, RNA binding protein 2 2.93 cisplatin resistance associated 2.92 serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10 2.9 hypothetical protein FLJ20920 2.86 disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila) 2.85 KIAA0318 protein 2.84 protein kinase C, delta 2.82 keratin 8 2.81 KIAA0633 protein 2.81 monoglyceride lipase 2.8 melanoma antigen, family D, 1 2.71 butyrophilin, subfamily 3, member A2 2.69 G protein-coupled receptor 116 2.66 proteasome (prosome, macropain) subunit, beta type, 8 (large multifunctional protease 7) 2.64 lymphotoxin beta (TNF superfamily, member 3) 2.63 hypothetical protein FLJ11132 2.62 hypothetical protein FLJ20896 2.62 homeo box C4 2.6 hypothetical gene CG018 2.59 N-acylaminoacyl- 2.56 potassium inwardly-rectifying channel, subfamily J, member 3 2.56 occludin 2.54 CamKI-like protein kinase 2.52 Homo sapiens mRNA from chromosome 5q31-33 region, mRNA sequence 2.48 acetyl-Coenzyme A acyltransferase 1 (peroxisomal 3-oxoacyl-Coenzyme A thiolase) 2.45 development and differentiation enhancing factor 2 2.43 potassium voltage-gated channel, subfamily H (eag-related), member 6 2.43 nipsnap homolog 1 (C. elegans) 2.42 RetII [Homo sapiens], mRNA sequence 2.42 Consensus includes gb:X75940.1 /DEF=H.sapiens beta glucuronidase pseudogene. /FEA=mRNA /DB_XREF=gi:1052700 /UG=Hs.324728 SMA5 2.41 protein tyrosine phosphatase, receptor type, F 2.4 KIAA0843 protein 2.39 homeodomain interacting protein kinase 2 2.39 interleukin 22 receptor, alpha 1 2.38

Suppl. Table 3 (continued)

Fold Change GI- Gene carcinoids/PNET LPS-induced TNF-alpha factor 2.37 KIAA0342 gene product 2.37 core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related 2.36 syndecan 4 (amphiglycan, ryudocan) 2.34 ATP-binding cassette, sub-family C (CFTR/MRP), member 6 2.34 PTPRF interacting protein, binding protein 1 (liprin beta 1) 2.33 RNA-binding protein gene with multiple splicing 2.29 synaptotagmin XIII 2.27 major histocompatibility complex, class I, E 2.24 mannosidase, alpha, class 2A, member 1 2.23 KIAA1598 protein 2.2 small optic lobes homolog (Drosophila) 2.19 F-box and -rich repeat protein 7 2.19 adducin 3 (gamma) 2.18 RAP1A, member of RAS oncogene family 2.17 G protein-coupled receptor kinase 5 2.14 Homo sapiens, clone IMAGE:4296901, mRNA, mRNA sequence 2.12 ubiquitin-activating E1-like 2.1 checkpoint suppressor 1 2.05 protein kinase C, eta 2.04 containing 2.01 potassium channel, subfamily K, member 1 2 NDRG family member 2 2 KIAA0820 protein 2 hypothetical protein PRO1635 2 four and a half LIM domains 1 1.99 cadherin 6, type 2, K-cadherin (fetal kidney) 1.97 Beta II spectrin [Homo sapiens], mRNA sequence 1.92 fasciculation and elongation protein zeta 2 (zygin II) 1.89 vinexin beta (SH3-containing adaptor molecule-1) 1.82

Supplemetary Table 4: Significantly downregulated genes in GI carcinoids when compared to PNETs (p<0.05)

Fold Change Gene PNET/GI carcinoids CGI-31 protein 0.57 chromosome 14 open reading frame 32 0.57 seven transmembrane domain protein 0.56 small nuclear ribonucleoprotein polypeptide F 0.56 ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptide 0.55 dynactin 3 (p22) 0.55 HSPC009 protein 0.55 hypothetical protein FLJ10846 0.55 chromosome 4 open reading frame 1 0.55 cytochrome c oxidase subunit VIb 0.54 secretory carrier membrane protein 1 0.54 hypothetical protein MGC4825 0.54 testis enhanced gene transcript (BAX inhibitor 1) 0.54 containing TCP1, subunit 8 (theta) 0.54 G protein-coupled receptor, family C, group 5, member C 0.54 sorcin 0.53 asparaginyl-tRNA synthetase 0.53 myosin VI 0.53 regulated PA26 nuclear protein 0.53 microtubule-associated protein, RP/EB family, member 1 0.53 dolichyl-diphosphooligosaccharide-protein glycosyltransferase 0.53 S- A4 0.52 methionyl aminopeptidase 2 0.52 hypothetical protein MGC14433 0.52 hypothetical protein ORF3 0.52 Hypothetical protein [Homo sapiens], mRNA sequence 0.52 ubiquitin-like 5 0.52 mitochondrial Rho 1 0.52 Huntingtin interacting protein K 0.52 hypothetical protein DC50 0.52 inositol polyphosphate-5-phosphatase, 72kDa 0.51 solute carrier family 11 (proton-coupled divalent metal ion transporters), member 2 0.51 unr-interacting protein 0.51 malic enzyme 3, NADP(+)-dependent, mitochondrial 0.51 ESTs, Highly similar to A47102 system b(0,+) amino acid transporter- involved protein - human [H.sapiens] 0.51 hypothetical protein DKFZp564D172 0.51 Consensus includes gb:AC005339 /DEF=Homo sapiens , cosmid R33729 /FEA=CDS /DB_XREF=gi:3355454 /UG=Hs.296443 hypothetical protein R33729_1 0.51 ubiquitin-like 3 0.51 phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase 0.51 Homo sapiens cDNA FLJ31079 fis, clone HSYRA2001595, mRNA sequence 0.51

Suppl. Table 4 (continued)

Fold Change Gene PNET/GI carcinoids Ras-related GTP-binding protein 0.50 tubulin-specific chaperone a 0.50 -tRNA synthetase 0.50 P58/GTA protein kinase [Homo sapiens], mRNA sequence 0.50 KIAA0368 protein 0.50 hypothetical protein DKFZp761N09121 0.50 hypothetical protein FLJ23560 0.50 lysosomal-associated membrane protein 2 0.50 F-box only protein 21 0.50 cytochrome c oxidase subunit VIIa polypeptide 2 (liver) 0.50 G protein-coupled receptor 107 0.50 KIAA0895 protein 0.50 coated vesicle membrane protein 0.49 ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F6 0.49 phosphatidylinositol glycan, class B 0.49 mitochondrial ribosomal protein L42 0.49 hypothetical protein HSPC111 0.49 surfeit 1 0.49 eukaryotic translation initiation factor 3, subunit 6 interacting protein 0.49 protein translocation complex beta 0.49 KIAA0222 gene product 0.49 ATPase, H+ transporting, lysosomal interacting protein 1 0.49 UDP-galactose transporter related 0.48 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6, 17kDa 0.48 golgin-67 0.48 STRIN protein 0.48 eukaryotic translation 1 epsilon 1 0.48 6-pyruvoyltetrahydropterin synthase 0.48 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 2, 8kDa 0.48 KIAA1254 protein 0.48 triad nucleotide binding protein 1 0.48 small nuclear ribonucleoprotein D1 polypeptide 16kDa 0.48 hypothetical protein BM-002 0.48 chromobox homolog 4 (Pc class homolog, Drosophila) 0.48 type I transmembrane receptor (seizure-related protein) 0.48 uracil-DNA glycosylase 0.47 cytochrome c, somatic 0.47 far upstream element (FUSE) binding protein 3 0.47 zinc finger protein 302 0.47 membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6) 0.47 neural stem cell derived neuronal survival protein 0.47 hypoxia up-regulated 1 0.47 hypothetical protein FLJ21613 similar to rat corneal wound healing related protein 0.47 par-3 partitioning defective 3 homolog (C. elegans) 0.47 inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein 0.47 glucose regulated protein, 58kDa 0.47

Suppl. Table 4 (continued)

Fold Change Gene PNET/GI carcinoids hypothetical protein FLJ10656 0.47 hypothetical protein FLJ22060 0.47 hypothetical protein FLJ21616 0.47 peptidylprolyl B (cyclophilin B) 0.46 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 7, 14.5kDa 0.46 tyrosine 3-monooxygenase/ 5-monooxygenase activation protein, theta polypeptide 0.46 Homo sapiens mRNA; cDNA DKFZp564D016 (from clone DKFZp564D016), mRNA sequence 0.46 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 chromosome 22 Contains a pseudogene similar to ribosomal protein L35, ESTs, STSs and GSSs 0.46 integral membrane protein 2B 0.46 G1 to S phase transition 2 0.46 ubiquitin-conjugating enzyme HBUCE1 0.46 carnitine deficiency-associated gene expressed in ventricle 1 0.46 leucine-rich PPR-motif containing 0.46 adenosine monophosphate deaminase 2 (isoform L) 0.46 proteasome (prosome, macropain) subunit, beta type, 7 0.45 carboxypeptidase D 0.45 inhibitor of Bruton's tyrsoine kinase 0.45 Homo sapiens mRNA; cDNA DKFZp586D0923 (from clone DKFZp586D0923), mRNA sequence 0.45 ret finger protein 2 0.45 cell death-regulatory protein GRIM19 0.45 likely ortholog of mouse WD-40-repeat-containing protein with a SOCS box 2 0.45 retinoic acid induced 17 0.45 vacuolar proton-ATPase subunit 0.45 EBNA-2 co-activator (100kD) 0.44 hypoxanthine phosphoribosyltransferase 1 (Lesch-Nyhan syndrome) 0.44 amyloid beta (A4) precursor-like protein 2 0.44 multiple inositol polyphosphate histidine phosphatase, 1 0.44 chemokine (C-X3-C motif) ligand 1 0.44 oculocerebrorenal syndrome of Lowe 0.44 Sec61 gamma 0.44 pyrophosphatase (inorganic) 0.44 HSPC125 protein 0.44 SEC24 related gene family, member D (S. cerevisiae) 0.43 NADH dehydrogenase (ubiquinone) 2, 24kDa 0.43 hypothetical protein LOC57821 0.44 kelch-like 3 (Drosophila) 0.43 Homo sapiens calmodulin-I (CALM1) mRNA, 3'UTR, partial sequence, mRNA sequence 0.43 ATPase, Na+/K+ transporting, alpha 1 polypeptide 0.43

Suppl. Table 4 (continued)

Fold Change Gene PNET/GI carcinoids ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscle 0.43 stress 70 protein chaperone, microsome-associated, 60kDa 0.43 hypothetical protein FLJ20534 0.43 peroxiredoxin 2 0.42 ATPase, H+ transporting, lysosomal interacting protein 2 0.42 hypothetical protein FLJ10769 0.42 similar to S. pombe dim1+ 0.42 transmembrane trafficking protein 0.42 calcium and integrin binding 1 (calmyrin) 0.42 chromosome 14 open reading frame 2 0.42 nudix (nucleoside diphosphate linked moiety X)-type motif 9 0.42 dicarbonyl/L-xylulose reductase 0.41 APMCF1 protein 0.41 Homo sapiens calmodulin-I (CALM1) mRNA, 3'UTR, partial sequence, mRNA sequence 0.41 p53-induced protein PIGPC1 0.41 DnaJ (Hsp40) homolog, subfamily B, member 9 0.40 Homo sapiens mRNA; cDNA DKFZp586A0618 (from clone DKFZp586A0618), mRNA sequence 0.40 chromosome 12 open reading frame 8 0.40 Bernardinelli-Seip congenital lipodystrophy 2 (seipin) 0.40 ral guanine nucleotide dissociation stimulator 0.40 KIAA0515 protein 0.40 Rap2 binding protein 9 0.40 interleukin 20 receptor, alpha 0.40 mesoderm specific transcript homolog (mouse) 0.39 kinesin 2 60/70kDa 0.39 KIAA0970 protein 0.39 hypothetical protein FLJ20559 0.39 forkhead box O1A (rhabdomyosarcoma) 0.39 protein phosphatase 2A, regulatory subunit B' (PR 53) 0.39 retinol dehydrogenase 11 (all-trans and 9-cis) 0.39 hypothetical protein FLJ21127 0.39 hypothetical protein FLJ20706 0.39 ATP citrate 0.39 dolichyl-phosphate mannosyltransferase polypeptide 3 0.39 ring finger protein (C3H2C3 type) 6 0.38 chitobiase, di-N-acetyl- 0.39 UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 6 0.38 hypothetical protein FLJ20375 0.38 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 8, 19kDa 0.38 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 similar to RPS17 0.38 RAB3A, member RAS oncogene family 0.37

Suppl. Table 4 (continued)

Fold Change Gene PNET/GI carcinoids kelch-like 2, Mayven (Drosophila) 0.37 parvin, beta 0.36 Homo sapiens mRNA; cDNA DKFZp564D016 (from clone DKFZp564D016), mRNA sequence 0.36 procollagen-, 2-oxoglutarate 4-dioxygenase (proline 4- hydroxylase), beta polypeptide (protein disulfide isomerase; thyroid hormone binding protein p55) 0.36 glycogenin 0.36 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 0.36 LIV-1 protein, estrogen regulated 0.36 myeloid leukemia factor 1 0.36 serine protease inhibitor, Kunitz type, 2 0.35 aspartate beta-hydroxylase 0.35 Consensus includes gb:V00489 /DEF=Human alpha-globin gene with flanks /FEA=mRNA /DB_XREF=gi:28548 /UG=Hs.272572 hemoglobin, alpha 2 0.35 very low density lipoprotein receptor 0.35 kinase insert domain receptor (a type III receptor tyrosine kinase) 0.35 NK6 transcription factor related, locus 1 (Drosophila) 0.34 Consensus includes gb:AF059180 /DEF=Homo sapiens mutant beta- globin (HBB) gene, complete cds /FEA=mRNA /DB_XREF=gi:4837722 /UG=Hs.155376 hemoglobin, beta 0.34 ESTs 0.34 integral type I protein 0.33 low density lipoprotein-related protein-associated protein 1 (alpha-2- macroglobulin receptor-associated protein 1) 0.33 chimerin (chimaerin) 1 0.33 phosphoribosyl pyrophosphate synthetase 1 0.32 glucokinase (hexokinase 4, maturity onset diabetes of the young 2) 0.32 transmembrane protein 4 0.32 secreted protein of unknown function 0.31 antigen identified by monoclonal antibodies 12E7, F21 and O13 0.31 Rag D protein 0.31 sialyltransferase 8C (alpha2,3Galbeta1,4GlcNAcalpha 2,8- sialyltransferase) 0.31 , member RAS oncogene family 0.30 Hemoglobin gamma-G [Homo sapiens], mRNA sequence 0.29 MAGE-E1 protein 0.29 putative L-type neutral amino acid transporter 0.28 tubulin-specific chaperone c 0.28 undifferentiated embryonic cell transcription factor 1 0.28 signal sequence receptor, delta (translocon-associated protein delta) 0.28 SH3-domain GRB2-like 2 0.27 calcium channel, voltage-dependent, P/Q type, alpha 1A subunit 0.27 SH3-domain GRB2-like endophilin B1 0.27 discoidin domain receptor family, member 1 0.25 Homo sapiens clone 23809 mRNA sequence 0.25

Suppl. Table 4 (continued)

Fold Change Gene PNET/GI carcinoids nucleolar protein 4 0.24 Williams Beuren syndrome chromosome region 14 0.23 KIAA1155 protein 0.23 secretogranin III 0.22 ESTs, Weakly similar to hypothetical protein FLJ22184 [Homo sapiens] [H.sapiens] 0.22 tropomodulin 0.22 KIAA0450 gene product 0.20 G-protein coupled receptor 0.19 p21 (CDKN1A)-activated kinase 3 0.18 KIAA0534 protein 0.18 zinc finger protein 204 0.18 cholinergic receptor, nicotinic, alpha polypeptide 5 0.17 forkhead box A2 0.17 carboxypeptidase E 0.17 pleiomorphic adenoma gene-like 1 0.16 eukaryotic translation elongation factor 1 alpha 2 0.15 cyclin-dependent kinase 5, regulatory subunit 1 (p35) 0.15 neuronal pentraxin II 0.14 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 0.12 endoplasmic reticulum oxidoreductin 1-Lbeta 0.08 dipeptidylpeptidase VI 0.06 ATP-binding cassette, sub-family C (CFTR/MRP), member 8 0.03 insulin 0.002