Associated Network Functions Score Focus Molecules Molecules in Network Proteins common to both pools Cell-To-Cell Signaling and Interaction, Hematological System Development and Function 47 29 26s Proteasome, A2M, APOB, APOE, APOH, C3, C5, CFB, F2, F10, F11, HABP2, ITLN1, LCN2, LTF,MIF, MPO, MUC5AC/MUC5B, PLG,PON1, PRDX1, PROC, PROS1, RBP4, SERPINA1, SERPINC1, SERPING1, SMPD2,TF Cellular Assembly and Organization, Cellular Function and Maintenance, Cellular Movement 40 28 ACTB, Actin, ACTN1, APOD, C2, C9, CAP1, CD55, CD59, CLU, EN01, Factin, FBLN1, FLNA, FN1, GAPDH, GSN, HBG1, HSP90AB1, Iti, ITIH1, ITIH2, LCP1, MDK, MUC4, NPC2, PGK1, VTN, YWHAZ Cancer 23 18 AHSG, ALB, APOA2, C1R, C1S, C4BPA, CD163, CFHR1, Fibrinogen, FOLR1, HPX, ITIH4, KLKB1, KNG1, MUC4, ORM1, SERPINA1, SERPINA3 Cell-To-Cell Signaling and Interaction, Hematological System Development and Function 18 15 AMBP, C1QA, C8A, CD163, CP, HRG, IGHA1, IGHA2, IGHG2, PGD, PGLYRP2, PIGR, PRDX2, TAP2, TUBB4B Proteins detected only in the benign pool Cellular Movement, Cell-To-Cell Signaling and Interaction, Tissue Development 43 25 ANXA1, C5, CD55, CD59, CDH13, CLU, DMBT1, DUOX2, EPS8L2, EZR, FBLN1, GNAI3, GNB2, GSN, MSN, MUC1, MUC4, RAC1, RAP1A, RAP1B, RDX, SDCBP, SPARC,SPP1, THY1 Cell Death and Survival 15 12 ACE,A NXA4, BAIAP2, C7, CHI3L1, FBLN2, GNA13, IFITM2, PDCD6IP, PROM1, SPARCL1, UBA52 Carbohydrate Metabolism, Lipid Metabolism, Small Molecule Biochemistry 14 12 APOA2, C4B (includes others), CFB, COL1A2, CST3, GNAQ, HPX,LDL, MUC16, PIGR, QSOX1, TM4SF1 Cellular Movement 14 11 ADAM9, ANXA2, CTSB, FN1, KRT19, OLFM4, S100A6, SLC9A3R1, SMPDL3B, SNX18, TTR Proteins detected only in the malignant pool Protein Synthesis, Molecular Transport, Protein Trafficking 43 30 ACTB, Actin,ACTR3, CAP1, ENO1, ERCC6, FASN, FGG, FLNA, GAPDH, GNB2L1, HNRNPA1, HNRNPK, HNRNPU, ILF3, KPNB1, MAP4, NCL, NPM1, NUMA1, NUTF2, OTUB1, PKM, PLEC, RPS8, RPS14, SSB, TAGLN2, XPO1, YBX1 Cell-To-Cell Signaling and Interaction, Tissue Development, Cellular Movement 41 29 ACTN4, ARHGDIA, C5, CALR, CAT, CDH5, CORO1A, EEF1A1, F10, Fibrinogen, FLNB, FN1, GP1BA, GPI, KNG1, LBP, LTF, MBL2, MCAM, MMP9, MPO, NAMPT, PROC, PSMB9, RHOA, RPS3A, SPTAN1, VCL, VCP Post-Translational Modification, Protein Folding 26 21 ANXA5, CAPZA1, CD44, CRP, CTTN, CYCS, FActin, HNRNPD, Hsp27, Hsp70, Hsp90, HSP90AB1, HSPA5, HSPA8, HSPB1,Igm, LCP1, LDL, NONO, PPIA, RPL6, SOD1, TIMP1,TLN1,TUBA1A, YWHAQ Cell-To-Cell Signaling and Interaction, Hematological System Development and Function, Immune Cell Trafficking 16 16 APOA4, APOM, ARPC2, DEFA1 (includes others), EEF1A2, GPLD1, HNRNPAB, Iti,ITIH1, ITIH2, LAP3, PSMB8, PSMB9, PSME2, PTGDS, SERPINA3 Cell Morphology 14 14 APOE, ARHGEF2, C4BPB, CSE1L, EIF3A, FKBP4, HIST1H2BB, LDHB, PARK7, PLTP, RALY, TMSB10/TMSB4X, UCHL1, USP5

Table 2: Networks list. Principal networks of common proteins detected in both pools and proteins observed only in the benign fluid pool and only in the malignant fluid pool using Ingenuity Pathways Analysis (IPA).