Supplementary Table 1 Genes tested in qRT-PCR in NFPAs Gene Bank accession Gene 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 protein BAX NM_004324 House design Bcl-2 binding component 3 BBC3 NM_014417.2 Hs00248075_m1 B-cell 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 receptor CXADR NM_001338.3 Hs00154661_m1 Homo sapiens Dicer1, Dcr-1 homolog (Drosophila) (DICER1) DICER1 NM_177438.1 Hs00229023_m1 Homo sapiens dystonin DST NM_015548.2 Hs00156137_m1 fms-related tyrosine kinase 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 microtubule-associated protein 1 light chain 3 beta MAP1LC3B NM_022818.3 Hs00797944_s1 matrix metallopeptidase 17 MMP17 NM_016155.4 Hs01108847_m1 myosin 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 botulinum toxin 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 enzyme 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 chromosome 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 sorting nexin 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 Cohen syndrome 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 p53 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 zinc finger 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 clock (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).