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Supplemental Table 6 Parent or Parent or Parent Child Child Lowest Mean Median Patient Patient Patient Parent Child Child Path Patient 1 Patient 1 Patient 2 Patient 2 Patient 2 Patient 3 PathwayName PathwayID Pathway in Pathway in Pathway in Level Pathway Pathway Patient 1 Gene List Patient 2 Gene List Patient 3 Gene List 1 2 3 PathwayID PathwayID Pathway in Length Uniprot List Targetome Uniprot List Targetome Uniprot List Targetome PathwayID PathwayID PathwayID Pathway Score Score PathwayID Unique R-HSA- R-HSA- Acetylation NA NA 1 FALSE NA FALSE FALSE FALSE 2 TRUE 1 1 NA NA NA NA NA NA P18440 NAT1,AAC1 NA 156582 156580 Butyrophilin (BTN) R-HSA- R-HSA- 1 NA NA FALSE NA FALSE FALSE FALSE 12 TRUE 1.41666667 1 Q8WVV5 BTN2A2,BT2.2,BTF2 NA NA NA NA NA NA NA family interactions 8851680 1280218 Carboxyterminal post-translational R-HSA- R-HSA- Q3ZCM7,Q8 2 1 1 FALSE NA FALSE FALSE FALSE 38 TRUE 2.71052632 1 TUBB8,TTLL11,C9orf20 NA Q8IUZ0 LRRC49 NA Q5VU57 AGBL4,CCP6 NA modifications of 8955332 597592 NHH1 tubulin P11168,P14 SLC2A2,GLUT2,SLC2A4, Cellular hexose R-HSA- R-HSA- NA 1 3 FALSE NA FALSE FALSE FALSE 22 TRUE 1.86363636 1 NA NA NA A0PJK1 SLC5A10,SGLT5 NA 672,Q9NY6 GLUT4,SLC2A8,GLUT8,G NA transport 189200 425407 4 LUTX1 Chondroitin sulfate R-HSA- R-HSA- CSGALNACT2,CHGN2,G 1 NA NA FALSE NA FALSE FALSE FALSE 20 TRUE 5 1 Q8N6G5 NA NA NA NA NA NA NA biosynthesis 2022870 1793185 ALNACT2,PRO0082 Cytosolic iron- R-HSA- R-HSA- P18074,P53 ERCC2,XPD,XPDC,NUBP1 sulfur cluster NA NA 2 FALSE NA FALSE FALSE FALSE 13 TRUE 6.15384615 1 NA NA NA NA NA NA NA 2564830 1430728 384 ,NBP,NBP1 assembly Cytosolic R-HSA- R-HSA- R-HSA- SULT1B1,ST1B2,SULT1B sulfonation of NA NA 1 FALSE FALSE FALSE FALSE 24 TRUE 1.875 1 NA NA NA NA NA NA O43704 NA 156584 156580 174362 2 small molecules Estrogen R-HSA- R-HSA- CYP19A1,ARO1,CYAR,CY 1 NA 1 FALSE NA FALSE FALSE FALSE 6 TRUE 1.83333333 1 P11511 NA NA NA NA C9JRZ8 AKR1B15 NA biosynthesis 193144 196071 P19 Gap junction R-HSA- R-HSA- R-HSA- P36383,Q8 1 NA 2 FALSE FALSE FALSE FALSE 19 TRUE 1.78947368 1 Q3ZCM7 TUBB8 NA NA NA NA GJC1,GJA7,GJD3,GJA11 NA assembly 190861 190828 190827 N144 Gap junction R-HSA- R-HSA- R-HSA- P36383,Q8 1 NA 2 FALSE FALSE FALSE FALSE 19 TRUE 1.78947368 1 Q3ZCM7 TUBB8 NA NA NA NA GJC1,GJA7,GJD3,GJA11 NA assembly 190861 190828 190704 N144 Gap junction R-HSA- R-HSA- R-HSA- P36383,Q8 1 NA 2 FALSE FALSE FALSE FALSE 19 TRUE 1.78947368 1 Q3ZCM7 TUBB8 NA NA NA NA GJC1,GJA7,GJD3,GJA11 NA assembly 190861 190828 190872 N144 R-HSA- R-HSA- R-HSA- Glucuronidation 1 NA NA FALSE FALSE FALSE FALSE 24 TRUE 1.41666667 1 P35504 UGT1A5,GNT1,UGT1 NA NA NA NA NA NA NA 156588 156580 173599 R-HSA- R-HSA- HCN channels NA NA 1 FALSE NA FALSE FALSE FALSE 4 TRUE 1 1 NA NA NA NA NA NA Q9Y3Q4 HCN4 NA 1296061 1296071 IL-6-type cytokine R-HSA- R-HSA- receptor ligand 1 NA NA FALSE NA FALSE FALSE FALSE 17 TRUE 6 1 P42702 LIFR NA NA NA NA NA NA NA 6788467 6783589 interactions Interaction With R-HSA- R-HSA- ADAM30,UNQ2509/PRO 1 NA 1 FALSE NA FALSE FALSE FALSE 10 TRUE 1.7 1 Q9UKF2 NA NA NA NA Q9UKJ8 ADAM21 NA The Zona Pellucida 1300644 1187000 5997 Intracellular R-HSA- R-HSA- NA NA 1 FALSE NA FALSE FALSE FALSE 3 TRUE 1.33333333 1 NA NA NA NA NA NA Q9NPG2 NGB NA oxygen transport 8981607 382551 P19013,P78 KRT4,CYK4,KRT85,KRTH O43790,Q8 KRT86,KRTHB6,KRT73,K KRTAP4- R-HSA- R-HSA- R-HSA- 386,Q02487 B5,DSC2,CDHF2,DSC3,KR Keratinization 4 1 5 FALSE TRUE TRUE TRUE 217 TRUE 1.60829493 1 6Y46,Q9945 6IRS3,KB36,KRT6IRS3,K NA Q9BYQ5 6,KAP4.15,KRTAP4- NA NA 6805567 1266738 6809371 ,Q86Y46,Q9 T73,K6IRS3,KB36,KRT6I 6,Q99959 RT12,PKP2 15,KRTAP4.15,KRTAP4.6 9569 RS3,PKP4 Miscellaneous R-HSA- R-HSA- transport and NA NA 1 FALSE NA FALSE FALSE FALSE 24 TRUE 1.375 1 NA NA NA NA NA NA Q7RTP0 NIPA1,SPG6 NA 5223345 382551 binding events Mitochondrial R-HSA- R-HSA- Q5JPH6,Q96 EARS2,KIAA1970,MARS tRNA 2 1 NA FALSE NA FALSE FALSE FALSE 21 TRUE 1.28571429 1 NA Q9NP81 SARS2,SARSM NA NA NA NA 379726 379724 GW9 2 aminoacylation Q15700,Q6 O14490,Q1 DLGAP1,DAP1,GKAP,GRI Neurexins and R-HSA- R-HSA- DLG2,SYT10,NRXN3,KIA 4 NA 3 FALSE NA FALSE FALSE FALSE 57 TRUE 3.66666667 1 XYQ8,Q9HD NA NA NA NA 2879,Q9NS N2A,NMDAR2A,HOMER NA neuroligins 6794361 6794362 A0743,C14orf60 B5,Q9Y4C0 C5 3 Phenylalanine and R-HSA- R-HSA- tyrosine NA NA 1 FALSE NA FALSE FALSE FALSE 11 TRUE 1.45454545 1 NA NA NA NA NA NA Q16773 KYAT1,CCBL1 NA 71182 6788656 catabolism Post-translational modification: R-HSA- R-HSA- R-HSA- LY6G6C,C6orf24,G6C,NG NA NA 1 FALSE TRUE TRUE TRUE 94 TRUE 1.60638298 1 NA NA NA NA NA NA O95867 NA synthesis of GPI- 163125 597592 162710 24,UNQ1947/PRO4430 anchored proteins Post-translational modification: R-HSA- R-HSA- R-HSA- LY6G6C,C6orf24,G6C,NG NA NA 1 FALSE FALSE FALSE TRUE 94 TRUE 1.60638298 1 NA NA NA NA NA NA O95867 NA synthesis of GPI- 163125 597592 162791 24,UNQ1947/PRO4430 anchored proteins Post-translational modification: R-HSA- R-HSA- R-HSA- LY6G6C,C6orf24,G6C,NG NA NA 1 FALSE FALSE FALSE TRUE 94 TRUE 1.60638298 1 NA NA NA NA NA NA O95867 NA synthesis of GPI- 163125 597592 162699 24,UNQ1947/PRO4430 anchored proteins PTK6 Regulates R-HSA- R-HSA- Proteins Involved NA NA 1 FALSE NA FALSE FALSE FALSE 5 TRUE 3.6 1 NA NA NA NA NA NA O75525 KHDRBS3,SALP,SLM2 NA 8849468 8848021 in RNA Processing R-HSA- R-HSA- Purine salvage 1 NA 1 FALSE NA FALSE FALSE FALSE 13 TRUE 1.53846154 1 P23109 AMPD1 NA NA NA NA Q6DHV7 ADAL NA 74217 8956321 R-HSA- R-HSA- SDK interactions NA NA 1 FALSE NA FALSE FALSE FALSE 2 TRUE 1 1 NA NA NA NA NA NA Q58EX2 SDK2,KIAA1514 NA 373756 421270 Sphingolipid de R-HSA- R-HSA- 1 NA NA FALSE NA FALSE FALSE FALSE 44 TRUE 1.34090909 1 P48448 ALDH3B2,ALDH8 NA NA NA NA NA NA NA novo biosynthesis 1660661 428157 Striated Muscle R-HSA- R-HSA- P35609,Q00 ACTN2,MYBPC1,MYBPC NA NA 2 FALSE NA FALSE FALSE FALSE 34 TRUE 1.70588235 1 NA NA NA NA NA NA NA Contraction 390522 397014 872 S Synthesis of R-HSA- R-HSA- pyrophosphates in NA NA 1 FALSE NA FALSE FALSE FALSE 10 TRUE 1.4 1 NA NA NA NA NA NA Q13572 ITPK1 NA 1855167 1483249 the cytosol TET1,2,3 and TDG R-HSA- R-HSA- Q13569,Q6 TDG,TET2,KIAA1546,Nbl NA NA 2 FALSE NA FALSE FALSE FALSE 4 TRUE 2.25 1 NA NA NA NA NA NA NA demethylate DNA 5221030 212165 N021 a00191 tRNA modification R-HSA- R-HSA- R-HSA- Q7Z6V5,Q8I ADAT2,DEADC1,TRMT44 in the nucleus and 2 NA NA FALSE FALSE FALSE FALSE 43 TRUE 1.34883721 1 NA NA NA NA NA NA NA 6782315 72306 6782861 YL2 ,C4orf23,METTL19 cytosol Tryptophan R-HSA- R-HSA- P48775,Q16 NA NA 2 FALSE NA FALSE FALSE FALSE 14 TRUE 1.92857143 1 NA NA NA NA NA NA TDO2,TDO,KYAT1,CCBL1 NA catabolism 71240 6788656 773 Vitamin B1 R-HSA- R-HSA- (thiamin) NA NA 1 FALSE NA FALSE FALSE FALSE 5 TRUE 1 1 NA NA NA NA NA NA Q9BZV2 SLC19A3 NA 196819 196849 metabolism O95259,Q8 Voltage gated KCNH1,EAG,EAG1,KCNH R-HSA- R-HSA- O43525,P22 NCM2,Q8TD Potassium 2 NA 5 FALSE NA FALSE FALSE FALSE 43 TRUE 1.53488372 1 KCNQ3,KCNA4,KCNA4L NA NA NA NA 5,EAG2,KCNG4,KCNG3,K NA 1296072 1296071 459 N1,Q9H3M0 channels CNF1,KCNQ5 ,Q9NR82 R-HSA- R-HSA- Q8NE62,Q8 CHDH,SLC44A1,CD92,CD Choline catabolism 2 NA NA FALSE NA FALSE FALSE FALSE 6 TRUE 1.83333333 1.5 NA NA NA NA NA NA NA 6798163 71291 WWI5 W92,CTL1 LGI-ADAM R-HSA- R-HSA- LGI3,LGIL4,UNQ8190/P 1 NA 1 FALSE NA FALSE FALSE FALSE 14 TRUE 4.28571429 1.5 Q8N145 NA NA NA NA Q9P0K1 ADAM22,MDC2 NA interactions 5682910 1266738 RO23199 Receptor-type R-HSA- R-HSA- O94991,P23 SLITRK5,KIAA0918,LRRC tyrosine-protein 1 NA 2 FALSE NA FALSE FALSE FALSE 20 TRUE 3.15 1.5 P23468 PTPRD NA NA NA NA NA 388844 6794362 468 11,PTPRD phosphatases R-HSA- R-HSA- O14641,Q9 Signaling by Hippo NA NA 2 FALSE NA FALSE FALSE FALSE 20 TRUE 6 1.5 NA NA NA NA NA NA DVL2,AMOTL2,KIAA0989 NA 2028269 162582 Y2J4 ABC transporters R-HSA- R-HSA- in lipid 1 NA NA TRUE NA FALSE TRUE TRUE 18 TRUE 3.27777778 2 Q8IUA7 ABCA9 NA NA NA NA NA NA NA 1369062 382556 homeostasis P55285,Q12 CDH6,CDH17,CDH24,CDH Adherens junctions R-HSA- R-HSA- R-HSA- Q9ULB4,Q9 3 NA 2 FALSE FALSE FALSE FALSE 31 TRUE 3.03225806 2 864,Q86UP 11L,UNQ2834/PRO3400 NA NA NA NA CDH9,CDH7,CDH7L1 NA interactions 418990 421270 420597 ULB5 0 9 Amino acid P49448,Q16 synthesis and R-HSA- R-HSA- R-HSA- GLUD2,GLUDP1,KYAT1,C NA NA 3 FALSE FALSE FALSE FALSE 34 TRUE 2 2 NA NA NA NA NA NA 773,Q9Y3Q NA interconversion 70614 71291 977347 CBL1,NAALAD2 0 (transamination) ASB14,MGRN1,KIAA054 PSME3,PSMD2,TRAP2,T P61289,Q13 A6NK59,O6 4,RNF156,PSMA1,HC2,N RIP12,KIAA0045,ULF,HU Antigen 200,Q14669 0291,P2578 U,PROS30,PSC2,UBE2D1 WE1,KIAA0312,KIAA157 processing: ,Q7Z6Z7,Q8 R-HSA- R-HSA- 6,P51668,Q ,SFT,UBC5A,UBCH5,UBC 8,UREB1,HSPC272,UBR1 Ubiquitination & 7 1 9 FALSE NA FALSE FALSE FALSE 309 TRUE 17.4854369 2 PSMA1 Q9UJX4 ANAPC5,APC5 NA IWV7,Q8TB PSMD2 983168 983169 5GLZ8,Q6U H5A,HERC4,KIAA1593,LR ,LNX1,LNX,PDZRN2,UNQ Proteasome B1,Q96PU5, WE0,Q9Y29 SAM1,TAL,UNQ6496/PR 574/PRO1136,NEDD4L,K degradation Q9H765,Q9 7 O21356,BTRC,BTRCP,FB IAA0439,NEDL3,ASB8,PP UH77 W1A,FBXW1A 14212,KLHL3,KIAA1129 BBSome-mediated R-HSA- R-HSA- cargo-targeting to NA NA 1 FALSE NA FALSE FALSE FALSE 23 TRUE 4.08695652 2 NA NA NA NA NA NA P50991 CCT4,CCTD,SRB NA 5620922 5620920 cilium Cation-coupled R-HSA- R-HSA- Chloride NA NA 1 TRUE NA FALSE TRUE TRUE 7 TRUE 2 2 NA NA NA NA NA NA Q13621 SLC12A1,NKCC2 NA 426117 425393 cotransporters Cell-extracellular R-HSA- R-HSA- R-HSA- 1 NA NA FALSE FALSE FALSE FALSE 16 TRUE 4.375 2 Q14315 FLNC,ABPL,FLN2 NA NA NA NA NA NA NA matrix interactions 446353 446728 446388 Cell-extracellular R-HSA- R-HSA- R-HSA- 1 NA NA FALSE FALSE FALSE FALSE 16 TRUE 4.375 2 Q14315 FLNC,ABPL,FLN2 NA NA NA NA NA NA NA matrix interactions 446353 446728 446343 Citric acid cycle R-HSA- R-HSA- 1 NA NA FALSE NA FALSE
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