Supplementary Table 1 tested in qRT-PCR in NFPAs

Gene Bank accession Description number ABI assay ID a disintegrin-like and metalloprotease with thrombospondin type 1 motif 7 ADAMTS7 NM_014272.3 Hs00276223_m1 Rho guanine nucleotide exchange factor (GEF) 3 ARHGEF3 NM_019555.1 Hs00219609_m1 BCL2-associated X BAX NM_004324 House design Bcl-2 binding component 3 BBC3 NM_014417.2 Hs00248075_m1 B- CLL/lymphoma 2 BCL2 NM_000633 House design Bone morphogenetic protein 7 BMP7 NM_001719.1 Hs00233476_m1 CCAAT/enhancer binding protein (C/EBP), alpha CEBPA NM_004364.2 Hs00269972_s1 coxsackie virus and adenovirus CXADR NM_001338.3 Hs00154661_m1 Homo sapiens Dicer1, Dcr-1 homolog () (DICER1) DICER1 NM_177438.1 Hs00229023_m1 Homo sapiens dystonin DST NM_015548.2 Hs00156137_m1 fms-related tyrosine 3 FLT3 NM_004119.1 Hs00174690_m1 glutamate receptor, ionotropic, N-methyl D-aspartate 1 GRIN1 NM_000832.4 Hs00609557_m1 high-mobility group box 1 HMGB1 NM_002128.3 Hs01923466_g1 heterogeneous nuclear ribonucleoprotein U HNRPU NM_004501.3 Hs00244919_m1 insulin-like growth factor binding protein 5 IGFBP5 NM_000599.2 Hs00181213_m1 latent transforming growth factor beta binding protein 4 LTBP4 NM_001042544.1 Hs00186025_m1 -associated protein 1 light chain 3 beta MAP1LC3B NM_022818.3 Hs00797944_s1 matrix metallopeptidase 17 MMP17 NM_016155.4 Hs01108847_m1 VA MYO5A NM_000259.1 Hs00165309_m1 Homo sapiens nuclear factor (erythroid-derived 2)-like 1 NFE2L1 NM_003204.1 Hs00231457_m1 oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide) OGDH NM_002541.2 Hs00159768_m1 oxysterol binding protein OSBP NM_002556.2 Hs00387304_m1 phosphoinositide-3-kinase, catalytic, beta polypeptide PIK3CB NM_006219.1 Hs00178872_m1 Homo sapiens peroxiredoxin 2 PRDX2 NM_181738.1 Hs00428488_g1 RAB1, member RAS oncogene family RAB1A NM_004161.3 Hs00800204_s1 ras-related C3 substrate 1 (rho family, small GTP binding protein) RAC1 NM_006908.3 House design v-ski avian sarcoma viral oncogene homolog SKI NM_003036.1 Hs00161707_m1 synaptosomal-associated protein, 25kD SNAP25 NM_003081.2 Hs00268296_m1 SNAP-associated protein SNAPAP NM_012437.3 Hs00276176_m1 somatostatin receptor 1 SSTR1 NM_001049.2 Hs00265617_s1 thromboxane A synthase 1 TBXAS1 NM_030984.1 Hs00233423_m1 TRK-fused gene TFG NM_006070.4 Hs00607175_m1 ubiquitin-conjugating E2L 3 UBE2L3 NM_003347.2 Hs00748530_s1 uncoupling protein 3 UCP3 NM_022803.1 Hs00243297_m1 Housekeeping gene Ribosomal Phosphoprotein PO RPLO NM_001002 House design

Supplementary Table 2- Bioinformatic analysis results using Class Prediction analysis (BrB software) in 22 invasive and 18 non invasive NFPAs

Geom mean Geom mean Parametric of ratios in of ratios in t-value Description Gene symbol p-value invasive Non invasive tumors tumors

1 Homo sapiens dystonin (DST), transcript variant 1eA, -7.18 p < 0.000001 0.512 0.861 mRNA [NM_015548] DST 2 -6.82 p < 0.000001 0.576 0.975 hypothetical protein LOC284889 LOC284889

3 Homo sapiens 3 open reading frame 10 -6.57 p < 0.000001 0.511 0.785 (C3orf10), mRNA [NM_018462] C3orf10 4 -6.43 p < 0.000001 0.323 0.568 Unknown THC2174081 5 -6.34 p < 0.000001 0.423 0.679 ubiquitin-conjugating enzyme E2L 3 UBE2L3

6 Homo sapiens cDNA FLJ42306 fis, clone TRACH2001646. -6.15 p < 0.000001 0.543 0.879 [AK124299] PPM1A 7 -5.83 p < 0.000001 0.534 0.916 coxsackie virus and adenovirus receptor CXADR

8 full-length cDNA clone CS0DI054YK17 of Placenta Cot 25- -5.8 1,00E-06 0.465 0.697 normalized of Homo sapiens (human). [CR618720] CR618720

9 Homo sapiens cDNA FLJ34585 fis, clone KIDNE2008758. -5.77 1,00E-06 0.641 1.026 [AK091904] AK091904 10 -5.77 1,00E-06 0.622 0.887 C9orf10 protein C9orf10 11 -5.76 1,00E-06 0.401 0.654 Unknown A_24_P375076 12 -5.7 1,00E-06 0.552 0.893 Unknown A_24_P264597 13 -5.69 2,00E-06 0.563 0.83 TRK-fused gene TFG 14 -5.64 2,00E-06 0.475 0.768 RAB1, member RAS oncogene family RAB1A 15 -5.62 2,00E-06 0.47 0.781 LIN-7 protein 3 LIN7C 16 -5.57 2,00E-06 0.411 0.721 synaptosomal-associated protein, 25kD SNAP25

17 Homo sapiens 3 (SNX3), transcript variant 3, -5.54 2,00E-06 0.592 0.916 mRNA [NM_152828] SNX3

18 Homo sapiens Dicer1, Dcr-1 homolog (Drosophila) -5.49 3,00E-06 0.525 0.846 (DICER1), transcript variant 1, mRNA [NM_177438] DICER1

19 Homo sapiens hypothetical protein MGC29463 -5.43 3,00E-06 0.62 0.905 (MGC29463), mRNA [NM_152686] DNAJC18 20 -5.35 4,00E-06 0.539 0.929 KIAA0940 protein CPEB3 21 -5.31 5,00E-06 0.565 0.836 lysyl-tRNA synthetase KARS 22 -5.22 7,00E-06 0.635 0.92 selenoprotein T SELT

23 Homo sapiens 1 (COH1), transcript -4.96 1.5e-05 0.534 0.812 variant 2, mRNA [NM_184042] VPS13B 24 -4.93 1.6e-05 0.567 0.809 hypothetical protein LOC339210 LOC339210 25 -4.93 1.7e-05 0.594 0.932 KIAA0940 protein CPEB3

26 Homo sapiens retinoic acid induced 17 (RAI17), mRNA -4.93 1.7e-05 0.621 0.912 [NM_020338] RAI17 27 -4.92 1.7e-05 0.53 0.789 BCE-1 protein TLE4 Homo sapiens peroxiredoxin 2 (PRDX2), nuclear gene 28 encoding mitochondrial protein, transcript variant 3, mRNA -4.87 2,00E-05 0.475 0.743 [NM_181738] PRDX2 29 -4.84 2.2e-05 0.582 0.865 DnaJ (Hsp40) homolog, subfamily B, member 6 DNAJB6 30 -4.8 2.5e-05 0.574 0.871 regulated PA26 nuclear protein SESN1 31 -4.77 2.7e-05 0.493 0.759 hypothetical protein FLJ11220 RSBN1 32 -4.76 2.8e-05 0.537 0.792 3-phosphoinositide dependent protein kinase-1 PDPK1 33 -4.71 3.3e-05 0.687 1.001 similar to bA508N22.1 (HSPC025) LOC340947 34 -4.7 3.4e-05 0.551 0.819 KIAA0416 protein LRRTM2 35 -4.69 3.4e-05 0.541 0.8 hypothetical protein PRO1855 PRO1855 36 -4.68 3.6e-05 0.58 0.835 HT014 C1orf128 37 -4.65 4,00E-05 0.596 0.819 Unknown A_24_P417996 38 -4.64 4.1e-05 0.583 0.899 neurexin 1 NRXN1

39 -4.62 4.3e-05 0.572 0.826 Unknown ENST00000331458 40 -4.61 4.5e-05 0.627 0.98 F-box only protein 9 FBXO9 41 -4.6 4.6e-05 0.662 0.987 hypothetical protein MGC5391 SFT2D3 42 -4.59 4.8e-05 0.691 1.074 protein 347 ZNF347

43 ALU7_HUMAN (P39194) Alu subfamily SQ sequence -4.58 4.8e-05 0.642 0.943 contamination warning entry, partial (12%) [THC2206574] THC2206574 44 -4.56 5.2e-05 0.507 0.774 hypothetical protein MGC14961 NAV1 45 -4.54 5.5e-05 0.499 0.797 hypothetical gene supported by BX647608 LOC399959 46 -4.54 5.5e-05 0.436 0.677 Unknown A_24_P264004

47 DNA directed RNA polymerase II polypeptide J-related -4.53 5.7e-05 0.503 0.71 gene POLR2J2 48 -4.43 7.8e-05 0.436 0.725 (mouse) homolog CLOCK 49 -4.41 8.2e-05 0.383 0.758 KIAA0878 protein RHOBTB3

50 RL1X_HUMAN (Q02543) 60S ribosomal protein L18a, -4.4 8.4e-05 0.574 0.798 partial (98%) [THC2071427] THC2071427 51 -4.35 9.8e-05 0.565 0.788 Unknown A_24_P164815 52 -4.33 0.000103 0.944 1.305 signal recognition particle 9kD SRP9 53 -4.33 0.000105 0.311 0.585 serine/threonine kinase 9 CDKL5

54 -4.32 0.000109 0.655 0.908 membrane component, chromosome 11, surface marker 1 GPIAP1 55 -4.31 0.00011 0.57 0.823 MORF-related gene 15 MORF4L1 56 -4.31 0.000111 0.637 0.95 ribosomal protein S5 RPS5

57 Homo sapiens DKFZP564F0522 protein -4.3 0.000115 0.613 0.892 (DKFZP564F0522), mRNA [NM_015475] FAM98A 58 -4.26 0.000128 0.56 0.783 hypothetical protein MGC3121 MGC3121

59 protein kinase, cAMP-dependent, regulatory, type I, alpha -4.26 0.000129 0.636 0.928 (tissue specific extinguisher 1) PRKAR1A 60 -4.24 0.000136 0.539 0.869 formin 2 FMN2 61 -4.24 0.000137 0.539 0.77 phosphoinositide-3-kinase, catalytic, beta polypeptide PIK3CB 62 -4.22 0.000147 0.516 0.806 hypothetical protein DKFZP434I0714 DKFZP434I0714 63 -4.2 0.000153 0.539 0.818 Unknown A_24_P384422

64 Homo sapiens WNK lysine deficient protein kinase 3 -4.18 0.000166 0.418 0.719 (WNK3), transcript variant 1, mRNA [NM_020922] WNK3

65 ALU1_HUMAN (P39188) Alu subfamily J sequence -4.16 0.000175 0.555 0.843 contamination warning entry, partial (6%) [THC2054351] THC2054351 66 -4.15 0.00018 0.717 0.971 mammalian inositol hexakisphosphate kinase 2 IHPK2 67 -4.14 0.000185 0.683 0.94 fused toes (mouse) homolog FTS

68 Homo sapiens clone FLC0675 PRO2870 mRNA, complete -4.13 0.000191 0.502 0.715 cds. [AF130080] AF130080 69 -4.13 0.000191 0.554 0.785 DKFZP586G1722 protein C1orf43

70 BIM_HUMAN (O43521) Bcl-2-like protein 11 (Bcl2 -4.11 0.000202 0.633 0.947 interacting mediator of cell death), complete [THC2172353] THC2172359 71 -4.11 0.000202 0.622 0.877 similar to hypothetical protein MNCb-2386 MED8 72 -4.11 0.000203 0.636 0.869 ribosomal protein L18a RPL18A 73 Homo sapiens hypothetical protein LOC127262 -4.08 0.000223 0.566 0.815 (LOC127262), mRNA [NM_182752] FAM79A 74 -4.08 0.000225 0.452 0.714 Kaiso ZBTB33 75 -4.06 0.000237 0.662 0.929 hypothetical protein HSPC177 CHMP5

76 -4.04 0.000251 0.547 0.869 sodium channel, voltage-gated, type III, alpha polypeptide SCN3A 77 -4.03 0.000256 0.521 0.813 ribosomal protein S6 kinase, 90kD, polypeptide 5 RPS6KA5 78 -4.02 0.000268 0.685 0.98 p53 regulated PA26 nuclear protein SESN1

79 Homo sapiens mRNA; cDNA DKFZp547H074 (from clone -3.96 0.000317 0.572 0.933 DKFZp547H074). [AL834407] UNC13C 80 -3.95 0.000327 0.675 0.952 hypothetical protein LOC92482 LOC92482 81 -3.94 0.000339 0.662 0.929 A kinase (PRKA) anchor protein 10 AKAP10 82 -3.94 0.000342 0.499 0.739 3 (NAD+) gamma IDH3G Homo sapiens protein kinase (cAMP-dependent, catalytic) 83 inhibitor gamma (PKIG), transcript variant 1, mRNA -3.92 0.000357 0.495 0.704 [NM_181805] PKIG 84 -3.92 0.000362 0.524 0.777 Unknown A_24_P24142

85 membrane protein (CD46, trophoblast-lymphocyte -3.91 0.000368 0.598 0.831 cross-reactive antigen) MCP

86 12 (HTF4, helix-loop-helix transcription -3.85 0.000434 0.644 0.914 factors 4) TCF12

87 Cbp/p300-interacting transactivator, with Glu/Asp-rich -3.84 0.000447 0.406 0.697 carboxy-terminal domain, 1 CITED1 88 -3.84 0.000448 0.476 0.69 Unknown A_24_P324214 89 -3.84 0.000457 0.544 0.803 hypothetical protein C14orf129 90 -3.82 0.000483 0.546 0.825 Unknown A_24_P280953

91 -3.78 0.000542 0.756 1.058 GIOT-2 for gonadotropin inducible transcription repressor-2 ZNF44 92 -3.78 0.000543 0.611 0.871 hypothetical protein LOC144363 LOC144363 93 -3.77 0.000547 0.573 0.829 t-complex 1 TCP1 94 -3.76 0.000568 0.537 0.757 inner , mitochondrial (mitofilin) IMMT 95 -3.76 0.000577 0.513 0.722 hypothetical protein MGC13098 MGC13098

96 RS2_HUMAN (P15880) 40S ribosomal protein S2 (S4) -3.75 0.000593 0.555 0.827 (LLREP3 protein), partial (41%) [THC2122491] THC2122491 97 -3.73 0.000625 0.627 0.881 similar to protein 40kD LOC391462 98 -3.73 0.000628 0.595 0.804 butyrate-induced transcript 1 PTPLAD1 99 -3.72 0.000644 0.723 1.041 eukaryotic translation elongation factor 1 alpha 1 EEF1A1 100 -3.72 0.000646 0.45 0.649 Unknown A_24_P307424

101 Homo sapiens zinc finger with KRAB and SCAN domains 1 -3.72 0.000647 0.792 1.139 (ZKSCAN1), mRNA [NM_003439] ZKSCAN1 102 -3.72 0.00065 0.595 0.858 butyrophilin, subfamily 3, member A2 BTN3A2 103 -3.71 0.000655 0.714 0.948 Unknown A_24_P324644 104 -3.7 0.000684 0.692 0.956 Unknown A_24_P195510

105 THAP domain containing 5 [Homo sapiens]. -3.69 0.000698 0.814 1.145 [Source:RefSeq;Acc:NM_182529] [ENST00000313516] THAP5

106 Homo sapiens cDNA FLJ31107 fis, clone IMR322000152. -3.66 0.000774 0.639 0.901 [AK055669] AK055669 107 -3.65 0.000774 0.581 0.773 antigen identified by monoclonal antibody MRC OX-2 CD200 108 -3.64 0.000809 0.463 0.677 Unknown A_24_P853302 109 -3.62 0.00085 0.529 0.775 ribosomal protein S2 RPS2 110 -3.6 0.000907 0.659 0.92 Unknown A_24_P144275 Homo sapiens ubiquitin-like, containing PHD and RING 111 finger domains, 2 (UHRF2), transcript variant 1, mRNA -3.59 0.000943 0.493 0.722 [NM_152306] UHRF2 112 -3.59 0.000944 0.564 0.77 KIAA0182 protein KIAA0182

113 Homo sapiens SON DNA binding protein (SON), transcript -3.58 0.000949 0.617 0.845 variant e, mRNA [NM_058183] SON Homo sapiens cDNA FLJ11804 fis, clone HEMBA1006272, 114 moderately similar to RETROVIRUS-RELATED 3.57 0.00099 1.632 1.183 (EC 3.4.23.-). [AK021866] AK021866

115 Homo sapiens hypothetical protein DKFZp547I048 3.59 0.000921 1.881 0.968 (DKFZp547I048), mRNA [NM_001002912] C1orf173 116 3.6 0.000918 2.04 1.289 hypothetical gene supported by AK091508 LOC441421 117 3.6 0.000911 1.448 1.086 marapsin PRSS27 118 3.64 8,00E-04 1.848 1.388 chromobox homolog 1 (Drosophila HP1 beta) CBX1 119 3.66 0.000759 1.533 0.966 hypothetical protein DKFZp313P036 DKFZp313P036 120 3.67 0.000733 1.661 1.215 hypothetical protein FLJ14549 ZNF206 121 3.68 0.000722 1.676 1.041 insulin-like growth factor binding protein 5 IGFBP5

122 Homo sapiens cDNA FLJ25091 fis, clone CBL09413. 3.69 0.000699 2.015 1.227 [AK057820] AK057820 123 Homo sapiens mRNA; cDNA DKFZp779E0216 (from clone 3.72 0.000635 2.057 1.486 DKFZp779E0216). [BX647217] HNRPA3 124 3.74 0.000614 1.66 1.118 neurogenin 3 NEUROG3

125 full-length cDNA clone CS0DI006YL02 of Placenta Cot 25- 3.74 0.00061 1.355 0.996 normalized of Homo sapiens (human). [CR607811] CR607811 126 3.74 0.000604 1.477 1.041 mitochondrial ribosomal protein L49 MRPL49 127 3.74 0.000601 1.578 1.127 Unknown THC2057861 128 3.75 0.000592 1.339 0.865 selenoprotein M SELM

129 HSMPP10 M phase phosphoprotein 10 {Homo sapiens;} , 3.76 0.000573 1.614 1.072 partial (31%) [THC2137463] ENST00000340049 130 3.77 0.000554 2.209 1.465 hypothetical LOC375010 LOC375010

131 Homo sapiens mitochondrial mRNA for AD 1, partial cds. 3.77 0.00055 0.924 0.569 [AB017116] MTND3 132 3.8 0.000524 1.567 1.152 KIAA1856 protein KIAA1856

133 3.8 0.000538 1.292 0.934 Homo sapiens, clone IMAGE:5311619, mRNA. [BC039450] BC039450 134 3.82 0.000481 1.425 1.031 sel-1 (suppressor of lin-12, C.elegans)-like SEL1L AA219130 zq99g05.s1 Stratagene NT2 neuronal precursor 135 937230 Homo sapiens cDNA clone IMAGE:650168 3', 3.83 0.000466 1.296 0.879 mRNA sequence [AA219130] AA219130 136 3.84 0.000464 1.495 1.072 similar to double protein LOC399839

137 Homo sapiens Humanin (HN1) mRNA, complete cds. 3.87 0.000417 1.162 0.695 [AY029066] AY029066 BM547196 AGENCOURT_6499364 NIH_MGC_124 Homo 138 sapiens cDNA clone IMAGE:5730270 5', mRNA sequence 3.87 0.000427 1.652 1.187 [BM547196] BM547196 139 3.88 0.000404 1.371 0.993 RP42 homolog DCUN1D1

140 Homo sapiens zinc finger protein 575 (ZNF575), mRNA 3.89 0.000394 1.52 1.089 [NM_174945] ZNF575 141 3.89 0.000392 1.358 0.746 hypothetical gene supported by AK128318 LOC389607 142 3.89 0.000401 1.639 1.181 Unknown A_32_P233211 143 3.89 0.000387 1.705 1.211 Unknown A_32_P61074 Homo sapiens ribosomal protein L10, mRNA (cDNA clone 144 IMAGE:4499390), with apparent retained intron. 3.9 0.000381 1.598 1.162 [BC021806] RPL10 145 similar to PSD-95/SAP90-associated protein-3 (R. 3.9 0.000388 1.51 1.093 norvegicus) from clone 24861 DLGAP3 146 3.91 0.000364 1.402 1.034 A, alpha (-binding protein-280) FLNA

147 3.92 0.000373 1.58 1.151 Unknown ENST00000325814 148 3.94 0.00034 1.491 1.053 oxysterol binding protein OSBP 149 3.95 0.000327 1.543 1.081 creatine kinase, brain CKB 150 4.01 0.000276 1.292 0.932 hypothetical gene LOC283846 DKFZp547E087 151 4.02 0.000268 1.584 1.135 similar to RIKEN cDNA A930017N06 gene LOC346355 152 4.06 0.000235 1.449 1.065 Wolf-Hirschhorn syndrome candidate 1-like 1 WHSC1L1

153 chromatin-specific transcription elongation factor, 140 kDa 4.08 0.000226 2.005 1.527 subunit SUPT16H

154 Homo sapiens, clone IMAGE:5221276, mRNA, partial cds. 4.08 0.000233 1.662 1.186 [BC028232] BC028232 155 4.08 0.000224 1.667 1.151 T-box 3 (ulnar mammary syndrome) TBX3

156 Homo sapiens tripartite motif-containing 35 (TRIM35), 4.09 0.000217 1.544 1.128 transcript variant 1, mRNA [NM_015066] TRIM35

157 tyrosine 3-monooxygenase/tryptophan 5-monooxygenase 4.1 0.000213 2.06 1.212 activation protein, gamma polypeptide YWHAG 158 4.1 0.000208 1.57 1.151 tenascin XB TNXB 159 4.12 0.000196 1.665 1.163 Unknown A_32_P1291 160 4.12 0.000196 1.583 1.072 mannosidase, alpha, class 1B, member 1 MAN1B1

161 Homo sapiens heterogeneous nuclear ribonucleoprotein A3 4.12 0.000195 2.022 1.438 (HNRPA3), mRNA [NM_194247] HNRPA3 RC1=NADH dehydrogenase subunit 3 homolog/ND3 162 homolog [human, renal cell carcinoma, mRNA 4.13 0.000191 1.835 0.943 Mitochondrial Partial, 65 nt]. [S81524] S81524

163 solute carrier family 8 (sodium/calcium exchanger), 4.15 0.000182 1.483 1.048 member 1 SLC8A1 164 4.16 0.000174 1.883 1.2 RPL13-2 LOC283345 AI878825 au50b09.y1 Schneider fetal brain 00004 Homo 165 sapiens cDNA clone IMAGE:2518169 5', mRNA sequence 4.16 0.000173 1.55 1.088 [AI878825] AI878825 166 4.16 0.000173 1.548 1.109 hypothetical protein LOC255783 LOC255783 167 4.17 0.000193 1.709 1.163 Unknown A_32_P112100 168 4.17 0.000172 1.727 1.225 bromodomain-containing 3 BRD3 169 4.18 0.000166 1.588 1.113 Unknown A_24_P461664 170 4.18 0.000165 1.807 1.224 hypothetical protein MGC4170 GNPTAB 171 4.19 0.000166 1.622 1.142 hypothetical protein MGC10772 PRR7 172 4.19 0.000159 1.619 1.145 BCL2-associated X protein BAX 173 4.22 0.000148 1.651 1.181 proline rich protein 5 PRR5 174 4.25 0.000132 1.673 0.962 ncaml LOC51328

175 4.26 0.000128 1.513 1.083 Homo sapiens KIAA1407 (KIAA1407), mRNA [NM_020817] KIAA1407

176 Human HL14 gene encoding beta-galactoside-binding 4.29 0.00012 1.632 1.138 lectin, 3' end, clone 2. [M14087] M14087 177 4.29 0.000117 1.453 1.038 capping protein (actin filament), -like CAPG 178 4.3 0.000116 1.581 1.093 Bcl-2 binding component 3 BBC3

179 Homo sapiens, clone IMAGE:4819956, mRNA, partial cds. 4.31 0.000112 1.64 1.158 [BC018035] BC018035 180 4.31 0.000116 1.605 1.118 Unknown A_32_P71864 181 4.33 0.000106 2.166 1.52 hypothetical protein SP329 FBXO38 182 4.35 9.9e-05 1.599 1.149 immediate early response 5 IER5

183 4.36 0.000101 1.592 1.136 Unknown ENST00000360262

184 Q8MRY2 (Q8MRY2) SD14156p, partial (7%) 4.39 8.8e-05 1.751 1.116 [THC2074889] THC2074889 185 4.39 8.7e-05 1.755 1.179 centrosomal protein 2 CEP2 Homo sapiens chromosome 9 open reading frame 62, 186 mRNA (cDNA clone MGC:35463 IMAGE:5193354), 4.41 8.3e-05 1.56 1.093 complete cds. [BC034752] C9orf62 187 4.45 7.3e-05 1.719 1.208 golgi autoantigen, golgin subfamily a, 3 GOLGA3 188 4.46 7.1e-05 1.677 1.191 hypothetical LOC439951 protein LOC439951 NADH-ubiquinone chain 3 (EC 1.6.5.3). 189 [Source:Uniprot/SWISSPROT;Acc:P03897] 4.49 6.4e-05 1.067 0.749 [ENST00000361227] SH3KBP1

190 Q7Z5X4 (Q7Z5X4) -like protein 4.5 6.3e-05 1.997 1.005 MGC:2625, isoform 1, partial (12%) [THC2080894] THC2080894 191 4.5 6.3e-05 1.647 1.16 hypothetical protein FLJ10490 FLJ10490 192 MMU19031 Smage-1 protein {Mus musculus;} , partial (6%) 4.5 6.2e-05 1.655 1.136 [THC2099668] THC2099668 193 4.52 5.9e-05 1.598 1.123 Unknown THC2175925

194 Homo sapiens ring finger and KH domain containing 1 4.57 5,00E-05 1.771 1.247 (RKHD1), mRNA [NM_203304] RKHD1 195 4.6 4.6e-05 2.388 1.575 KIAA1671 protein KIAA1671 196 4.62 4.3e-05 1.953 1.289 family member 3B KIF3B

197 Homo sapiens protein phosphatase 1K (PP2C domain 4.64 4.1e-05 1.66 0.842 containing) (PPM1K), mRNA [NM_152542] PPM1K 198 4.65 4.2e-05 1.64 1.168 G protein-coupled receptor 48 LGR4

199 BC001487 TARDBP protein {Homo sapiens;} , partial 4.66 3.8e-05 2.032 1.423 (68%) [THC2087278] ENST00000315091 200 4.71 3.3e-05 1.918 1.365 chromobox homolog 1 (Drosophila HP1 beta) CBX1 201 4.71 3.3e-05 1.749 1.219 Unknown A_32_P101073 202 4.73 3.1e-05 2.204 1.176 ARHGEF5-like FLJ43692

203 BC041700 rabaptin, GTPase binding effector protein 4.74 3,00E-05 1.781 1.282 1 {Homo sapiens;} , complete [THC2016168] THC2016168

204 Q6NVT1 (Q6NVT1) MGC69319 protein, partial (3%) 4.74 3,00E-05 1.92 1.269 [THC2199258] THC2199258 205 4.74 3,00E-05 1.899 1.155 Unknown A_24_P358305 206 4.75 2.9e-05 1.755 1.211 hypothetical protein FLJ22184 FLJ22184 207 4.75 2.9e-05 1.741 1.124 chromobox homolog 5 (Drosophila HP1 alpha) CBX5 208 4.76 2.8e-05 1.707 1.16 winged helix/forkhead transcription factor FOXQ1 209 4.77 2.7e-05 1.525 1.05 SRY (sex determining region Y)-box 1 SOX1

210 4.78 2.6e-05 1.604 1.112 par-6 (partitioning defective 6, C.elegans) homolog gamma PARD6G

211 MUSHSP84B heat-shock protein hsp84 {Mus musculus;} , 4.8 2.5e-05 2.218 1.482 partial (17%) [THC2165212] THC2165212 212 4.81 3.7e-05 2.099 1.233 hypothetical protein LOC284072 LOC284072 213 4.81 2.4e-05 1.651 1.125 Unknown A_32_P171984 214 4.84 2.2e-05 1.49 1.027 hypothetical protein LOC283849 LOC283849 215 4.84 2.2e-05 2.104 1.456 KIAA1327 protein KIAA1327 216 4.84 2.2e-05 1.434 0.992 hypothetical protein LOC201175 LOC201175 217 4.84 2.2e-05 1.555 1.003 Ca2+-promoted Ras inactivator RASA4 218 4.85 2.1e-05 2.797 1.651 upstream regulatory element binding protein 1 HUWE1 219 4.85 2.1e-05 1.622 1.105 SRY (sex determining region Y)-box 3 SOX3

220 4.86 2,00E-05 1.536 1.057 Homo sapiens mRNA for alternative form of GDNF; HFK4. GDNF 221 4.87 2,00E-05 1.799 1.097 complexin 2 CPLX2 222 4.87 2,00E-05 1.967 1.279 Unknown A_24_P922101 223 4.88 1.9e-05 1.864 1.32 ralA binding protein 1 RALBP1 Homo sapiens scavenger receptor cysteine rich domain 224 containing, group B (4 domains) (SRCRB4D), mRNA 4.88 1.9e-05 1.486 0.967 [NM_080744] SRCRB4D

225 Homo sapiens hypothetical protein FLJ31052 (FLJ31052), 4.89 1.9e-05 1.744 1.171 mRNA [NM_152378] FCRL2 226 4.89 1.8e-05 1.943 1.261 malignancy-associated protein MAG 227 4.92 1.7e-05 1.987 1.142 4 TPM4

228 Homo sapiens scratch homolog 2, zinc finger protein 4.95 1.6e-05 1.508 1.038 (Drosophila) (SCRT2), mRNA [NM_033129] SCRT2 229 4.95 1.7e-05 1.739 1.135 heparan sulfate 2-O-sulfotransferase HS2ST1 230 4.96 1.5e-05 1.629 1.133 cytochrome c oxidase subunit VIa polypeptide 2 COX6A2

231 Homo sapiens cDNA FLJ34218 fis, clone FCBBF3022311. 4.98 1.4e-05 1.58 1.061 [AK091537] C18orf23 232 4.98 1.4e-05 1.727 1.131 cell division cycle 2-like 2 CDC2L2 233 4.99 1.4e-05 2.618 1.496 myosin VA (heavy polypeptide 12, myoxin) MYO5A 234 5.03 1.3e-05 1.755 1.142 Unknown A_32_P132422

235 ALU1_HUMAN (P39188) Alu subfamily J sequence 5.03 1.2e-05 1.555 1.066 contamination warning entry, partial (10%) [THC2087262] THC2087262 236 5.06 1.1e-05 1.591 1.107 Unknown A_24_P780709

237 Homo sapiens H63 breast cancer expressed gene (H63), 5.08 1,00E-05 2.36 1.579 transcript variant 2, mRNA [NM_177974] CASC4

238 Q7Z0F7 (Q7Z0F7) Bindin (Fragment), partial (5%) 5.08 1.1e-05 1.721 1.172 [THC2182662] THC2182662

239 Q7U441 (Q7U441) Possible ABC transporter, ATP-binding 5.11 1,00E-05 1.549 0.925 component precursor, partial (8%) [THC2210612] THC2210612 240 5.11 9,00E-06 1.681 1.16 Unknown A_32_P65793

241 O17434 (O17434) Minor ampullate silk protein MiSp1 5.13 9,00E-06 1.705 1.093 (Fragment), partial (4%) [THC2097260] THC2097260 242 5.16 8,00E-06 2.024 1.236 RAB18, member RAS oncogene family RAB18

243 Homo sapiens open reading frame 86 5.18 8,00E-06 1.845 1.153 (C20orf86), mRNA [NM_080674] C20orf86 244 5.18 8,00E-06 2.12 1.387 heterogeneous nuclear ribonucleoprotein A0 HNRPA0 245 5.2 7,00E-06 1.674 1.125 hypothetical protein FLJ20640 C19orf24

246 full-length cDNA clone CS0DA001YA12 of Neuroblastoma 5.22 7,00E-06 2.304 1.466 of Homo sapiens (human). [CR616772] CR616772

247 AW386276 CM2-PT0015-141299-055-d11 PT0015 Homo 5.23 6,00E-06 1.969 1.127 sapiens cDNA, mRNA sequence [AW386276] AW386276 248 5.23 6,00E-06 1.699 1.077 CXYorf1-related protein FLJ00038 249 5.23 6,00E-06 1.807 1.198 peptide YY, 2 (seminalplasmin) PYY2 250 5.23 6,00E-06 1.841 1.081 similar to CG32542-PA LOC196752 251 5.24 6,00E-06 1.797 1.177 heat shock 90kD protein 1, alpha HSPCA

252 Homo sapiens cDNA FLJ40719 fis, clone THYMU2028379. 5.25 6,00E-06 1.763 1.204 [AK098038] C19orf31 253 5.25 6,00E-06 1.828 1.164 Unknown A_24_P641742

254 H.sapiens mRNA for CRF2 receptor, beta isoform, 5.27 6,00E-06 1.726 1.167 aberrantly spliced, (94bp ). [Y10152] Y10152 255 5.29 5,00E-06 1.964 1.26 proacrosin binding protein sp32 precursor ACRBP 256 5.3 5,00E-06 1.627 1.082 hypothetical protein FLJ12015 BAALC

257 Homo sapiens zinc finger protein, multitype 1 (ZFPM1), 5.31 5,00E-06 1.719 1.183 mRNA [NM_153813] ZFPM1 258 5.31 5,00E-06 1.635 1.069 Q15464 (Q15464) Shb, partial (4%) [THC2053095] THC2053095 259 5.34 5,00E-06 2.317 1.306 Human retinal pigment epithelium mRNA. [L07392] L07392 260 5.37 4,00E-06 2.571 1.315 hypothetical protein H41 H41 261 5.38 4,00E-06 1.873 1.15 Unknown A_23_P210297

262 5.38 4,00E-06 2.15 1.485 Unknown ENST00000339054 263 5.39 4,00E-06 1.885 1.213 similar to hypothetical protein FLJ13841 LOC146325

264 Homo sapiens zinc finger, DHHC domain containing 21 5.39 4,00E-06 1.823 1.188 (ZDHHC21), mRNA [NM_178566] ZDHHC21 265 5.4 4,00E-06 1.74 1.13 Unknown A_24_P714316 266 similar to protein phosphatase 1, regulatory (inhibitor) subunit 11 isoform 1; hemochromatosis candidate gene V; 5.4 4,00E-06 1.69 1.123 t-complex-associated-testis-expressed 5; inhibitor-3 LOC391014 267 5.44 3,00E-06 1.66 1.129 CCAAT/enhancer binding protein (C/EBP), alpha CEBPA 268 5.45 3,00E-06 1.464 0.977 Unknown THC2142362 269 5.45 3,00E-06 1.606 1.123 Unknown A_32_P230059

270 Homo sapiens ornithine decarboxylase antizyme 4 mRNA, 5.47 3,00E-06 1.791 1.198 complete cds. [AF293339] AF293339 271 5.49 3,00E-06 2.097 1.31 hypothetical protein FLJ14644 ZNF341 272 5.5 3,00E-06 1.613 1.049 RNA-binding protein S1, serine-rich domain RNPS1 Homo sapiens protein phosphatase 1, regulatory (inhibitor) 273 subunit 11 (PPP1R11), transcript variant 2, mRNA 5.51 3,00E-06 1.592 1.076 [NM_170781] PPP1R11

274 full-length cDNA clone CS0DE005YO06 of Placenta of 5.51 3,00E-06 2.476 1.496 Homo sapiens (human). [CR611094] CR611094 275 5.52 3,00E-06 2.265 1.321 scaffold attachment factor B SAFB 276 5.53 3,00E-06 1.526 0.945 Unknown THC2098338 277 5.56 2,00E-06 1.843 1.17 G protein-coupled receptor 12 GPR12 278 5.57 2,00E-06 1.835 1.169 hypothetical protein FLJ36701 FLJ36701 279 5.64 2,00E-06 1.977 1.205 Unknown A_32_P231880 280 5.65 2,00E-06 1.691 0.97 hypothetical protein FLJ31413 FLJ31413 281 5.65 2,00E-06 1.734 1.149 phosphofructokinase, liver PFKL

282 5.66 2,00E-06 1.776 1.084 Homo sapiens, clone IMAGE:5728979, mRNA. [BC035731] BC035731 283 5.67 2,00E-06 1.752 1.064 LOC399491 protein LOC399491 284 5.69 1,00E-06 1.807 1.091 basic-helix-loop-helix-PAS protein NPAS3 285 5.71 1,00E-06 2.719 1.672 heat shock 90kD protein 1, beta HSPCB 286 5.81 1,00E-06 1.836 1.143 radical fringe (Drosophila) homolog RFNG 287 5.81 1,00E-06 1.889 1.163 calcium channel, voltage-dependent, alpha 1E subunit CACNA1E

288 Homo sapiens zinc finger protein 579 (ZNF579), mRNA 5.83 p < 0.000001 1.879 1.147 [NM_152600] ZNF579

289 Homo sapiens cDNA FLJ25756 fis, clone TST06241. 5.85 p < 0.000001 2.36 1.272 [AK098622] PRTG 290 5.85 p < 0.000001 1.817 1.23 Unknown A_24_P927245 291 5.87 p < 0.000001 2.447 1.368 Homo sapiens tropomyosin 3 (TPM3), mRNA [NM_152263] TPM3

292 Homo sapiens forkhead-like 18 (Drosophila) (FKHL18), 5.89 p < 0.000001 1.765 1.15 mRNA [NM_004118] FKHL18

293 5.89 p < 0.000001 1.869 1.236 Unknown ENST00000334083

294 Homo sapiens serine/threonine protein kinase Kp78 splice 5.93 p < 0.000001 1.724 1.13 variant CTAK75a mRNA, complete cds. [AF159295] AF159295 295 5.93 p < 0.000001 1.635 0.989 nuclear pore complex interacting protein NPIP

296 Q6QAT0 (Q6QAT0) 60S ribosomal protein L32, partial 5.96 p < 0.000001 1.804 1.192 (35%) [THC2164098] THC2164098 297 5.98 p < 0.000001 1.855 1.123 hypothetical protein FLJ14464 PARP10 298 5.98 p < 0.000001 1.916 1.227 KIAA0872 protein MON1B

299 RME1_YEAST (P32338) Zinc finger protein RME1, partial 5.98 p < 0.000001 1.933 1.208 (5%) [THC2145096] THC2145096 300 6 p < 0.000001 2.896 1.372 v-ski avian sarcoma viral oncogene homolog SKI

301 Homo sapiens, clone IMAGE:5092955, mRNA, partial cds. 6.03 p < 0.000001 1.551 0.977 [BC034002] BC034002 302 6.05 p < 0.000001 1.771 1.138 hypothetical protein FLJ13111 FLJ13111 303 6.07 p < 0.000001 2.049 1.201 cyclin-dependent kinase 3 CDK3 304 6.08 p < 0.000001 1.779 1.088 Unknown A_32_P77759 305 6.1 p < 0.000001 2.102 1.186 hypothetical protein FLJ22938 C1orf113 306 6.14 p < 0.000001 2.428 1.259 valyl-tRNA synthetase 2 VARS 307 6.14 p < 0.000001 1.489 0.933 Unknown A_32_P114268

308 cholinergic receptor, nicotinic, beta polypeptide 2 6.15 p < 0.000001 2.016 1.174 (neuronal) CHRNB2

309 Homo sapiens regulator of G-protein signalling 3 (RGS3), 6.24 p < 0.000001 1.787 1.063 transcript variant 6, mRNA [NM_144488] RGS3 310 6.26 p < 0.000001 1.939 1.147 tryptase gamma 1 TPSG1

311 6.28 p < 0.000001 1.977 1.197 Unknown ENST00000355411

312 thromboxane A synthase 1 (platelet, cytochrome P450, 6.32 p < 0.000001 1.811 1.168 subfamily V) TBXAS1 313 Homo sapiens aldolase A, fructose-bisphosphate (ALDOA), 6.34 p < 0.000001 2.107 1.2 transcript variant 2, mRNA [NM_184041] ALDOA 314 6.34 p < 0.000001 2.115 1.212 calcium channel, voltage-dependent, alpha 1I subunit CACNA1I 315 6.34 p < 0.000001 1.96 1.108 ORF [NP111687] NP111687 316 6.34 p < 0.000001 1.683 1.071 fms-related tyrosine kinase 3 FLT3 317 6.35 p < 0.000001 2.631 1.159 uncoupling protein 3 (mitochondrial, proton carrier) UCP3 318 6.36 p < 0.000001 1.732 1.126 hypothetical protein DKFZp566J091 LBH 319 6.36 p < 0.000001 2.302 1.186 KIAA1545 protein KIAA1545 320 6.38 p < 0.000001 2.257 1.069 choline acetyltransferase CHAT

321 heterogeneous nuclear ribonucleoprotein U (scaffold 6.41 p < 0.000001 2.027 1.163 attachment factor A) HNRPU 322 6.41 p < 0.000001 2.009 1.24 similar to KIAA0592 protein LOC387680 323 6.42 p < 0.000001 1.617 0.985 KIAA0476 gene product KIAA0476 324 6.46 p < 0.000001 1.681 1.097 hypothetical protein FLJ38379 FLJ38379

325 Homo sapiens cDNA clone IMAGE:4329532, partial cds. 6.47 p < 0.000001 2.053 1.095 [BC011940] BC011940 326 6.54 p < 0.000001 1.895 1.039 DNA-binding transcriptional activator MYCNOS 327 6.57 p < 0.000001 2.113 1.277 Unknown A_24_P928250 Homo sapiens cDNA FLJ38910 fis, clone NT2NE2006813, 328 weakly similar to CELL SURFACE GLYCOPROTEIN 1 6.59 p < 0.000001 1.843 1.117 PRECURSOR. [AK096229] AK096229

329 Human clone pL713 hypothetical protein mRNA, partial 6.59 p < 0.000001 1.69 1.142 cds. [U12206] PABPN1 330 6.6 p < 0.000001 2.309 1.353 hypothetical protein FLJ14225 KIAA0319L 331 6.64 p < 0.000001 2.114 1.267 S100 calcium-binding protein A5 S100A5

332 Homo sapiens cDNA FLJ11976 fis, clone HEMBB1001253. 6.67 p < 0.000001 2.11 1.171 [AK022038] AK022038 333 6.7 p < 0.000001 2.201 1.153 hypothetical gene supported by BC031673 LOC389199 334 6.71 p < 0.000001 1.819 1.053 Homo sapiens NRF1 protein (NRF1) mRNA. NFE2L1 335 6.76 p < 0.000001 2.613 1.198 Unknown A_24_P7785

336 Q87TC7 (Q87TC7) General secretion pathway protein N, 6.83 p < 0.000001 2.209 1.107 partial (5%) [THC2134185] THC2134185 337 6.83 p < 0.000001 2.747 1.159 Unknown A_32_P185089 338 6.94 p < 0.000001 3.166 1.223 hypothetical protein MGC10334 MGC10334 339 6.96 p < 0.000001 2.48 1.288 Unknown A_24_P152278 340 6.98 p < 0.000001 2.127 1.193 LOC440504 LOC440504 341 6.99 p < 0.000001 2.464 1.284 ARS component B SLURP1

342 Q8MIF3 (Q8MIF3) Twist transcription factor, partial (7%) 7.03 p < 0.000001 2.426 1.151 [THC2105947] THC2105947

343 oxoglutarate (alpha-ketoglutarate) dehydrogenase 7.11 p < 0.000001 2.442 1.118 (lipoamide) OGDH

344 Homo sapiens late cornified envelope 1D (LCE1D), mRNA 7.21 p < 0.000001 2.64 1.188 [NM_178352] LCE1D

345 a disintegrin-like and metalloprotease (reprolysin type) with 7.55 p < 0.000001 3.365 1.23 thrombospondin type 1 motif, 7 ADAMTS7 346 7.69 p < 0.000001 1.988 1.198 hypothetical protein FLJ11730 C1orf149

Supplementary Table 3 Expression of Ki67, PTTG, MMP9, MYO5A and IGFBP5 in 6 non invasive NFPAs (numbered 1 to 6) and 5 invasive NFPAs (numbered 7 to 11) studied by immunohistochemistry. Both the percentage of labelled cells and the intensity of labelling are indicated

NFPAs Ki67 PTTG MMP9 MYO5A IGFBP5 10% 15% 10% 1% NEGATIVE 1 + + +

10% 25% 40% 5% NEGATIVE 2 + + +

5% 10% 5% 30% 1% 3 + + +/- +

40% 5% 55% 5% NEGATIVE 4 + +/- +

10% 10% 10% 70% 5% 5 +/- +/- +/- +

10 4% NEGATIVE NEGATIVE 30% 6 +

70% 5% 80% 50% 5% 7 + + + +

70% 20% 75% 40% 5% 8 + + ++ ++ +

Diffuse 5% 70% 100% 4% 9 + +/- + +

70% 1% 100% 50% 1% 10 + +/- ++ ++

50% 10% 70% 50% 1% 11 + + + +