Supplementary Table 2. List of stroma related genes (i.e. probe sets overexpressed in core relative to FNA biopsies of the same cancer) Probe set Name Symbol 1598_g_at growth arrest-specific 6 GAS6 200048_s_at jumping translocation breakpoint JTB 200054_at zinc finger protein 259 ZNF259 200055_at TAF10 RNA polymerase II, TATA box binding protein (TBP)-associatedTAF10 factor, 30kDa 200059_s_at ras homolog gene family, member A RHOA 200060_s_at RNA binding protein S1, serine-rich domain RNPS1 200070_at chromosome 2 open reading frame 24 C2orf24 200613_at adaptor-related protein complex 2, mu 1 subunit AP2M1 200663_at CD63 molecule CD63 200665_s_at secreted protein, acidic, cysteine-rich (osteonectin) SPARC 200671_s_at spectrin, beta, non-erythrocytic 1 SPTBN1 200696_s_at gelsolin (amyloidosis, Finnish type) GSN 200704_at lipopolysaccharide-induced TNF factor LITAF 200738_s_at phosphoglycerate kinase 1 PGK1 200760_s_at ADP-ribosylation-like factor 6 interacting protein 5 ARL6IP5 200762_at dihydropyrimidinase-like 2 DPYSL2 200770_s_at laminin, gamma 1 (formerly LAMB2) LAMC1 200771_at laminin, gamma 1 (formerly LAMB2) LAMC1 200772_x_at prothymosin, alpha PTMA 200778_s_at septin 2 2-Sep 200782_at annexin A5 ANXA5 200784_s_at low density lipoprotein-related protein 1 (alpha-2-macroglobulin receptor)LRP1 200785_s_at low density lipoprotein-related protein 1 (alpha-2-macroglobulin receptor)LRP1 200795_at SPARC-like 1 (hevin) SPARCL1 200799_at heat shock 70kDa protein 1A HSPA1A 200807_s_at heat shock 60kDa protein 1 (chaperonin) HSPD1 200811_at cold inducible RNA binding protein CIRBP 200813_s_at platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit PAFAH1B145kDa 200816_s_at platelet-activating factor acetylhydrolase, isoform Ib, alpha subunit PAFAH1B145kDa 200822_x_at triosephosphate isomerase 1 TPI1 200866_s_at prosaposin PSAP 200874_s_at NOP56 ribonucleoprotein homolog (yeast) NOP56 200875_s_at NOP56 ribonucleoprotein homolog (yeast) NOP56 200878_at endothelial PAS domain protein 1 EPAS1 200882_s_at proteasome (prosome, macropain) 26S subunit, non-ATPase, 4 PSMD4 200883_at ubiquinol-cytochrome c reductase core protein II UQCRC2 200896_x_at hepatoma-derived growth factor (high-mobility group protein 1-like) HDGF 200897_s_at palladin, cytoskeletal associated protein PALLD 200903_s_at S-adenosylhomocysteine hydrolase AHCY 200906_s_at palladin, cytoskeletal associated protein PALLD 200907_s_at palladin, cytoskeletal associated protein PALLD 200911_s_at transforming, acidic coiled-coil containing protein 1 TACC1 200931_s_at vinculin VCL 200951_s_at cyclin D2 CCND2 200953_s_at cyclin D2 CCND2 200954_at ATPase, H+ transporting, lysosomal 16kDa, V0 subunit c ATP6V0C 200966_x_at aldolase A, fructose-bisphosphate ALDOA 200971_s_at stress-associated endoplasmic reticulum protein 1 SERP1 200973_s_at tetraspanin 3 TSPAN3 200974_at actin, alpha 2, smooth muscle, aorta ACTA2 200982_s_at annexin A6 ANXA6 200984_s_at CD59 molecule, complement regulatory protein CD59 200986_at serpin peptidase inhibitor, clade G (C1 inhibitor), member 1 SERPING1 200997_at RNA binding motif protein 4 RBM4 201012_at annexin A1 ANXA1 201028_s_at CD99 molecule CD99 201034_at adducin 3 (gamma) ADD3 201041_s_at dual specificity phosphatase 1 DUSP1 201044_x_at dual specificity phosphatase 1 DUSP1 201046_s_at RAD23 homolog A (S. cerevisiae) RAD23A 201058_s_at myosin, light chain 9, regulatory MYL9 201061_s_at stomatin STOM 201069_at matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa typeMMP2 IV collagenase) 201105_at lectin, galactoside-binding, soluble, 1 LGALS1 201107_s_at thrombospondin 1 THBS1 201108_s_at thrombospondin 1 THBS1 201109_s_at thrombospondin 1 THBS1 201110_s_at thrombospondin 1 THBS1 201111_at CSE1 chromosome segregation 1-like (yeast) CSE1L 201116_s_at carboxypeptidase E CPE 201117_s_at carboxypeptidase E CPE 201119_s_at cytochrome c oxidase subunit 8A (ubiquitous) COX8A 201125_s_at integrin, beta 5 ITGB5 201133_s_at praja ring finger 2 PJA2 201137_s_at major histocompatibility complex, class II, DP beta 1 HLA-DPB1 201141_at glycoprotein (transmembrane) nmb GPNMB 201147_s_at TIMP metallopeptidase inhibitor 3 TIMP3 201148_s_at TIMP metallopeptidase inhibitor 3 TIMP3 201149_s_at TIMP metallopeptidase inhibitor 3 TIMP3 201150_s_at TIMP metallopeptidase inhibitor 3 TIMP3 201151_s_at muscleblind-like (Drosophila) MBNL1 201162_at insulin-like growth factor binding protein 7 IGFBP7 201163_s_at insulin-like growth factor binding protein 7 IGFBP7 201175_at thioredoxin-related transmembrane protein 2 TMX2 201185_at HtrA serine peptidase 1 HTRA1 201205_at ribosome binding protein 1 homolog 180kDa (dog) RRBP1 201215_at plastin 3 (T isoform) PLS3 201220_x_at C-terminal binding protein 2 CTBP2 201224_s_at serine/arginine repetitive matrix 1 SRRM1 201255_x_at HLA-B associated transcript 3 BAT3 201261_x_at biglycan BGN 201262_s_at biglycan BGN 201278_at disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)DAB2 201279_s_at disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)DAB2 201280_s_at disabled homolog 2, mitogen-responsive phosphoprotein (Drosophila)DAB2 201289_at cysteine-rich, angiogenic inducer, 61 CYR61 201300_s_at prion protein PRNP 201305_x_at acidic (leucine-rich) nuclear phosphoprotein 32 family, member B ANP32B 201307_at septin 11 11-Sep 201310_s_at chromosome 5 open reading frame 13 C5orf13 201324_at epithelial membrane protein 1 EMP1 201325_s_at epithelial membrane protein 1 EMP1 201326_at chaperonin containing TCP1, subunit 6A (zeta 1) CCT6A 201328_at v-ets erythroblastosis virus E26 oncogene homolog 2 (avian) ETS2 201329_s_at v-ets erythroblastosis virus E26 oncogene homolog 2 (avian) ETS2 201336_at vesicle-associated membrane protein 3 (cellubrevin) VAMP3 201337_s_at vesicle-associated membrane protein 3 (cellubrevin) VAMP3 201338_x_at general transcription factor IIIA GTF3A 201348_at glutathione peroxidase 3 (plasma) GPX3 201350_at flotillin 2 FLOT2 201357_s_at splicing factor 3a, subunit 1, 120kDa SF3A1 201368_at zinc finger protein 36, C3H type-like 2 ZFP36L2 201390_s_at casein kinase 2, beta polypeptide CSNK2B 201391_at TNF receptor-associated protein 1 TRAP1 201399_s_at translocation associated membrane protein 1 TRAM1 201403_s_at microsomal glutathione S-transferase 3 MGST3 201426_s_at vimentin VIM 201430_s_at dihydropyrimidinase-like 3 DPYSL3 201431_s_at dihydropyrimidinase-like 3 DPYSL3 201438_at collagen, type VI, alpha 3 COL6A3 201441_at cytochrome c oxidase subunit Vib polypeptide 1 (ubiquitous) COX6B1 201445_at calponin 3, acidic CNN3 201463_s_at transaldolase 1 TALDO1 201464_x_at jun oncogene JUN 201472_at von Hippel-Lindau binding protein 1 VBP1 201494_at prolylcarboxypeptidase (angiotensinase C) PRCP 201496_x_at myosin, heavy chain 11, smooth muscle MYH11 201497_x_at myosin, heavy chain 11, smooth muscle MYH11 201505_at laminin, beta 1 LAMB1 201508_at insulin-like growth factor binding protein 4 IGFBP4 201511_at angio-associated, migratory cell protein AAMP 201531_at zinc finger protein 36, C3H type, homolog (mouse) ZFP36 201539_s_at four and a half LIM domains 1 FHL1 201540_at four and a half LIM domains 1 FHL1 201551_s_at lysosomal-associated membrane protein 1 LAMP1 201558_at RAE1 RNA export 1 homolog (S. pombe) RAE1 201559_s_at chloride intracellular channel 4 CLIC4 201560_at chloride intracellular channel 4 CLIC4 201563_at sorbitol dehydrogenase SORD 201590_x_at annexin A2 ANXA2 201615_x_at caldesmon 1 CALD1 201616_s_at caldesmon 1 CALD1 201617_x_at caldesmon 1 CALD1 201621_at neuroblastoma, suppression of tumorigenicity 1 NBL1 201630_s_at acid phosphatase 1, soluble ACP1 201645_at tenascin C TNC 201647_s_at scavenger receptor class B, member 2 SCARB2 201655_s_at heparan sulfate proteoglycan 2 HSPG2 201666_at TIMP metallopeptidase inhibitor 1 TIMP1 201667_at gap junction protein, alpha 1, 43kDa GJA1 201669_s_at myristoylated alanine-rich protein kinase C substrate MARCKS 201677_at chromosome 3 open reading frame 37 C3orf37 201680_x_at serrate RNA effector molecule homolog (Arabidopsis) SRRT 201690_s_at tumor protein D52 TPD52 201694_s_at early growth response 1 EGR1 201708_s_at nipsnap homolog 1 (C. elegans) NIPSNAP1 201709_s_at nipsnap homolog 1 (C. elegans) NIPSNAP1 201718_s_at erythrocyte membrane protein band 4.1-like 2 EPB41L2 201719_s_at erythrocyte membrane protein band 4.1-like 2 EPB41L2 201739_at serum/glucocorticoid regulated kinase 1 SGK1 201743_at CD14 molecule CD14 201744_s_at lumican LUM 201749_at endothelin converting enzyme 1 ECE1 201751_at Josephin domain containing 1 JOSD1 201753_s_at adducin 3 (gamma) ADD3 201759_at tubulin folding cofactor D TBCD 201785_at ribonuclease, RNase A family, 1 (pancreatic) RNASE1 201787_at fibulin 1 FBLN1 201792_at AE binding protein 1 AEBP1 201796_s_at valyl-tRNA synthetase VARS 201798_s_at myoferlin MYOF 201809_s_at endoglin ENG 201811_x_at SH3-domain binding protein 5 (BTK-associated) SH3BP5 201827_at SWI/SNF related, matrix associated, actin dependent regulator of chromatin,SMARCD2 subfamily d, member 2 201839_s_at epithelial cell adhesion molecule EPCAM 201842_s_at EGF-containing fibulin-like extracellular matrix protein 1 EFEMP1 201843_s_at EGF-containing fibulin-like extracellular matrix protein 1 EFEMP1 201852_x_at collagen, type III, alpha 1 COL3A1 201853_s_at cell division cycle 25 homolog B (S. pombe) CDC25B 201860_s_at plasminogen activator, tissue PLAT 201893_x_at decorin DCN 201896_s_at proline/serine-rich coiled-coil 1 PSRC1 201912_s_at G1 to S phase transition 1 GSPT1 201913_s_at Coenzyme A synthase COASY 201953_at