Supplementary Table 1. Genes Significantly Upregulated in Expression in Retina Compared to FVMs Gene Fold Description RefSeq P -value Symbol change Visual perception Bestrophin 1 BEST1 NM_004183.2 4.07E-09 86.99 Retinal pigment epithelium-specific protein 65kDa RPE65 NM_000329.2 1.70E-10 86.03 Retinaldehyde binding protein 1 RLBP1 NM_000326.3 3.42E-07 84.89 Retinal G protein coupled receptor RGR NM_001012720.18.61E-09 55.26 Tyrosinase (oculocutaneous albinism IA) TYR NM_000372.4 1.94E-11 43.54 Carbonic anhydrase IV CA4 NM_000717.2 1.46E-06 36.98 Opticin OPTC NM_014359.3 4.78E-08 32.73 Retinol dehydrogenase 5 (11-cis/9-cis) RDH5 NM_002905.2 6.41E-07 26.23 Secreted frizzled-related protein 5 SFRP5 NM_003015.2 2.31E-08 25.48 Retinal outer segment membrane protein 1 ROM1 NM_000327.2 2.33E-06 15.08 Paired box 6, transcript variant 2 PAX6 NM_001604.3 1.03E-06 15.02 Bestrophin 2 BEST2 NM_017682.2 4.10E-09 12.70 Solute carrier family 45, member 2, transcript variant 1 SLC45A2 NM_016180.3 8.30E-09 12.12 Retina and anterior neural fold homeobox RAX NM_013435.2 7.62E-06 10.93 Retinol dehydrogenase 10 (all-trans) RDH10 NM_172037.2 1.34E-05 10.35 Retinal pigment epithelium-derived rhodopsin homolog RRH NM_006583.2 1.07E-06 10.16 Amine oxidase, copper containing 2 (retina-specific) AOC2 NM_001158.3 1.92E-08 9.48 Nervous system development Purkinje cell protein 4 PCP4 NM_006198.2 1.33E-05 70.59 Aldehyde dehydrogenase 1 family, member A2 ALDH1A2 NM_170697.1 5.08E-08 32.32 CD24 molecule CD24 NM_013230.2 1.46E-06 26.74 Endothelin 3 EDN3 NM_207032.1 1.89E-07 20.69 Cholinergic receptor, nicotinic, alpha 3. CHRNA3 NM_000743.2 1.24E-07 20.44 Cadherin 1, type 1, E-cadherin (epithelial) CDH1 NM_004360.2 1.47E-10 19.71 SRY (sex determining region Y)-box 10 SOX10 NM_006941.3 1.40E-08 18.40 Fas apoptotic inhibitory molecule 2 FAIM2 NM_012306.2 1.31E-05 15.84 Paired-like homeodomain 2 PITX2 NM_000325.5 2.63E-08 13.76 Chondroitin sulfate proteoglycan 5 (neuroglycan C) CSPG5 NM_006574.3 1.09E-08 11.41 Reelin RELN NM_173054.1 2.62E-07 10.15 NDRG family member 2 NDRG2 NM_201539.1 1.39E-05 9.86 Microtubule-associated protein tau MAPT NM_016841.2 5.61E-06 9.37 Transcription factor AP-2 alpha (activating enhancer TFAP2A NM_001032280.23.27E-10 9.36 binding protein 2 alpha) Metabolism 3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 HMGCS2 NM_005518.2 1.68E-09 57.48 (mitochondrial) Beta-carotene 15,15'-monooxygenase 1 BCMO1 NM_017429.2 5.50E-08 40.13 Solute carrier family 16, member 8 (monocarboxylic SLC16A8 NM_013356.2 1.49E-08 36.63 acid transporter 3) Apolipoprotein D APOD NM_001647.2 1.30E-05 36.59 Hydroxysteroid (17-beta) dehydrogenase 2 HSD17B2 NM_002153.1 1.86E-08 27.33 Creatine kinase, muscle CKM NM_001824.2 7.76E-10 17.97 ATPase, H+ transporting, lysosomal 42kDa, V1 ATP6V1C2 NM_144583.3 3.47E-09 16.28 ATPase, Na+/K+ transporting, beta 1 polypeptide ATP1B1 NM_001677.3 3.03E-07 13.73 Kallikrein-related peptidase 1 KLK11 NM_144947.1 1.28E-08 12.52 Solute carrier family 23 (nucleobase transporters), SLC23A2 NM_203327.1 9.22E-09 11.62 member 2 Carbonic anhydrase XIV CA14 NM_012113.1 7.77E-09 10.63 ATPase, class V, type 10B ATP10B NM_025153.2 7.15E-09 10.15 Tryptase alpha/beta 1 TPSAB1 NM_003294.3 1.33E-06 9.82 Transport Transthyretin (prealbumin, amyloidosis type I) TTR NM_000371.1 5.79E-11 261.60 Solute carrier family 39 (zinc transporter), member 12 SLC39A12 NM_152725.2 5.31E-11 33.92 Chloride intracellular channel 6 CLIC6 NM_053277.1 6.36E-06 28.99 Transient receptor potential cation channel, subfamily TRPM3 NM_206948.2 4.55E-10 20.14 M, member 3 Downloaded from iovs.arvojournals.org on 10/02/2021 Sodium channel, nonvoltage-gated 1 alpha SCNN1A NM_001038.4 8.88E-08 20.13 Potassium inwardly-rectifying channel, subfamily J, KCNJ13 NM_002242.2 7.96E-08 16.77 member 13 Solute carrier family 29 (nucleoside transporters), SLC29A4 NM_153247.1 2.32E-08 15.68 member 4. Solute carrier family 13 (sodium/sulfate symporters), SLC13A4 NM_012450.2 1.07E-08 13.20 member 4 Snaptoporin SYNPR NM_144642.3 3.31E-07 12.80 Solute carrier family 7, (neutral amino acid transporter, SLC7A10 NM_019849.1 2.23E-08 11.68 y+ system) member 10 Solute carrier family 22 (organic anion transporter), SLC22A8 NM_004254.2 2.61E-07 10.57 member 8 Cell differentiation silver homolog (mouse) SILV NM_006928.3 9.50E-11 195.09 Tyrosinase-related protein 1 TYRP1 NM_000550.1 1.70E-12 127.86 Paired-like homeodomain transcription factor 1 PITX1 NM_002653.3 1.69E-10 59.19 Scavenger receptor class A, member 5 (putative) SCARA5 NM_173833.4 2.23E-09 32.14 Dopachrome tautomerase (dopachrome delta- DCT NM_001922.2 3.47E-10 25.96 isomerase, tyrosine-related protein 2). Collagen, type IX, alpha 1,transcript variant 1 COL9A1 NM_001851.3 9.23E-10 20.14 melanophilin MLPH NM_001042467.15.79E-08 20.10 Glyceraldehyde-3-phosphate dehydrogenase, GAPDHS NM_014364.3 3.12E-09 19.99 spermatogenic Death associated protein-like 1 DAPL1 NM_001017920.15.26E-06 16.89 ATPase, Ca++ transporting, cardiac muscle, fast ATP2A1 NM_173201.2 2.30E-10 16.63 Cbp/p300-interacting transactivator, with Glu/Asp-rich CITED1 NM_004143.2 4.80E-08 15.58 carboxy-terminal domain, 1 EGF-like-domain, multiple 6 EGFL6 NM_015507.2 4.85E-06 14.95 Folate receptor 1 (adult) FOLR1 NM_016724.1 6.05E-08 13.79 Chromosome 4 open reading frame 31 C4orf31 NM_024574.3 9.11E-08 13.17 Septin 3 SEPT3 NM_019106.4 3.15E-07 9.74 Signaling Ectonucleotide pyrophosphatase/phosphodiesterase 2 ENPP2 NM_001040092.11.50E-07 22.17 (autotaxin) Gastrin-releasing peptide GRP NM_001012513.15.67E-06 14.45 DNA-damage-inducible transcript 4-like DDIT4L NM_145244.2 1.36E-07 12.68 Proenkephalin PENK NM_006211.2 4.66E-08 9.39 Anatomical structure development Sclerostin domain containing 1 SOSTDC1 NM_015464.2 1.90E-10 21.94 Myocilin, trabecular meshwork inducible glucocorticoid MYOC NM_000261.1 6.98E-11 19.44 response Forkhead box Q1 FOXQ1 NM_033260.3 1.16E-05 9.53 Development LIM domain only 1 (rhombotin 1) LMO1 NM_002315.1 2.75E-09 15.24 Immune response C3 and PZP-like, alpha-2-macroglobulin domain CPAMD8 NM_015692.2 7.50E-09 11.03 Stress response Tissue factor pathway inhibitor 2 TFPI2 NM_006528.2 5.34E-10 14.24 Unknown Hypothetical protein LOC285016 LOC285016 NM_001002919.15.63E-12 61.44 Melan-A MLANA NM_005511.1 5.76E-10 54.58 Tetraspanin 10 TSPAN10 NM_031945.3 1.06E-08 50.66 Similar to F-box only protein 2 LOC342897 NM_001001414.11.04E-10 27.96 Chromosome 2 open reading frame 40 C2orf40 NM_032411.1 9.17E-07 19.66 Mo sapiens FLJ42875 protein FLJ42875 XM_932794.1 1.25E-09 16.51 Transmembrane protein with EGF-like and two TMEFF2 NM_016192.2 8.16E-10 15.30 follistatin-like domains 2 CDNA FLJ38396 fis, clone FEBRA2007957 EST AK095715 1.07E-05 14.81 Reprimo-like RPRML NM_203400.1 7.86E-10 11.18 Downloaded from iovs.arvojournals.org on 10/02/2021 Supplementary Table 2. Top Key Biological Functions Related to Genes Upregulated in Expression in FVMs Compared to Retina Focus Functions Molecules in Network Score Molecules ADAMTS9,ANXA2,C1q,CD93,COL1A2,COL1A1 (includes EG:1277),COL4A1,collagen, Connective Tissue Disorders, Cellular Collagen Alpha1,Cyclin D,Ecm,ECM1(includesEG:100332249), ERK1/2,FAP,Fibrin, Assembly and Organization, Cellular HSD11B2,IGFBP3,Igfbp,IL-1R,ITGA11,LOX,LRRC32,MMP11,Nuclear 41 22 Function and Maintenance factor1,POSTN,SH2B3,Smad2/3, Smad2/3Smad4,SPRY4,SULF1,TFPI,Tgf beta,TNC (includes EG:116640),TRAM2,VCAN Alpha catenin,CCNB2,COL3A1,COL4A2,COL5A1,COL5A2,COL6A3,Collagen type I, Cell Morphology, Cellular Assembly and Collagen type III,Collagen type IV,Collagen Type V,Collagen Type VI,Collagen(s),GPIIB- Organization, Hair and Skin Development IIIA,Integrin,Integrin alpha 3 beta 1,Integrin alpha 4 beta 1,Integrin alpha 5 beta 35 18 and Function 1,Integrin,ITGA1,LAMA4,LAMB1,LAMC1,Laminin1,Laminin2,Laminin,LUM,MMP23B,NFkB (complex),PLAU,SERPINH1,THBS1,THBS2, THY1,TNFAIP6 Humoral Immune Response, Cellular 14-3-3,Actin,Akt,Alp,APLN,Cadherin,CALD1,CDH5,CDH13,DLX5,ESM1,Ifn gamma,Ige, Growth and Proliferation, Hematological IL32,JAG1,Mlc,MYO1B,Nfat (family),NFE2L3,NOX4,Pak,PECAM1,PI3K (family),PIK3CG, 32 19 System Development and Function Rap1,Rock,TCR,TES,Tnf,TNFRSF4,TNFSF4,TOP2A,TPM4,Tropomyosin,TRPC6 Ca2+,CACNA2D2,CALU,CAST,EBF2,EEF1B2,FKBP2,FKBP8,FKBP1A,GIPR,GLP1R,HAS Cell-To-Cell Signaling and Interaction, 2,HAUS4,KDELR3,KISS1,NEFM,PAX3,PCSK6,PIN4 (includes EG:43044),POLA1, PPIC, Reproductive System Development and 28 15 PRND,PTMA,PXDN,RAI14,RPP40,SAMD9,TBX15,THBS2,TNC (includes EG:116640), Function, Cell Signaling TPPP3,UBC,USP6,WDR41,YY1 AHR,AVIL,C1QTNF6,C21orf7,CCL23,Ck2,COL14A1,CST1,DNTTIP1,ESR1,ETS1,FOXC1, Cell Morphology, Digestive System GEMIN2,Histone h3,HNF1A,IFNG (includes EG:15978),IL13,Insulin,Interferon alpha, Development and Function, Hepatic System 24 14 LRRC17,NR5A2,OLFML2A,OSM,PAMR1,PCDH17,POU4F1,Proinsulin,PWP2,RNA Development and Function polymerase II,SPATA18,ST8SIA4,SUMO2,TIMP4,TNFAIP8L1,TP53 (includes EG:22059) 26s Proteasome,Alpha tubulin,AMPK,CD36,CDKN1A,Cyclin A,Cytochrome c,DYSF,E2f, Cell Cycle, Cellular Development, Cellular estrogen receptor,Hdac,Histone h4,Ifn,IgG1,IgG,Igm,IL12 (complex),IL12 (family), 23 13 Growth and Proliferation Immunoglobulin,KRT7,N-cor,NLRP3,PHLDA2,PI3K (complex),PRSS23,RUNX1,Rxr, SETD8,SKA2,SP100,SRC (family),Tlr,TRPS1,TSH,UBE2C ANGPT2,Ap1,Calcineurin protein(s),Caspase 3/7,Cg,Collagen type IX,Creb,ERK, Organismal Injury and Abnormalities, Fibrinogen,FJX1,FSH,Growth hormone,HDL,IL1,INHBB,ITGB1,LDL,Lh,MAP2K1/2 16 10 Cardiac Fibrosis, Cardiovascular Disease ,Mek,MMP9,NADPH oxidase,Pdgf (complex),PDGF BB,Pkc(s),PTPRE,SERPINE1, Smad,Sos,SPARC,SPRED1,STAT5a/b,thyroid hormone receptor,Tnf receptor,TRIP11 ADCY,ADORA3,ANO1,Calmodulin,calpain,caspase,CD3,ENTPD1,F2R,FAM48A,FNDC1,F Organismal Injury and Abnormalities, ocal adhesion kinase,G protein alphai,G protein beta gamma,Gpcr,GPR116,Hsp90, 14 9 Respiratory Disease, Molecular Transport Jnk,Mapk,Mmp,P110,P38 MAPK,p85 (pik3r),Pka,PLC,PLC gamma,PPEF1,Pro- inflammatory Cytokine,Rac,Ras,Ras homolog,Sfk,Shc,TRAF6,Vegf Downloaded from iovs.arvojournals.org on 10/02/2021 Supplementary Table 3.