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Compilation of AD-Associated and Non-AD Genes

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Compilation of AD-Associated and Non-AD Genes Compilation of AD-associated and non-AD genes AD-associated (positives) and non-AD (positives) genes are needed to build a machine learning model. First of all, we performed intensive hand-curation to identify confident AD-associated genes (positives) from various disease genes resources, including AlzGene1, AlzBase2, OMIM3, DisGenet4, DistiLD5, and UniProt6, Open Targets7, GWAS Catalog8, differentially expressed genes (DEGs) in ROSMAP9, and published literature. The curated genes from each resource as well as the corresponding criteria were provided in Table 1 in this file. As the AD-associated genes as well as their reliability vary across these resources, we used a vote strategy and selected only the genes that are present in at least two of the above-described resources to ensure higher reliability. In this way, we collected 147 AD-associated genes (Table 2). Of them, most (n=103, 70%) were associated with AD based on GWAS. Next, we selected a set of non-AD genes, (i.e. negatives), which refer to the genes that have no or minimal association with AD. The main idea of our method for non-AD gene selection was to remove any genes that exhibit potential associations with AD. Let Gp be the set of the 147 collected positives. We then selected a negative gene set GN containing genes that are potentially associated with AD in the following procedure. We first performed a Gene Ontology (GO) enrichment analysis for the positives using PANTHER10 and obtained 737 biological process terms (FDR<0.05). It is reasonable to assume that the genes annotated to these GO terms exhibit a potential association with AD compared with a random baseline because they were annotated to the same GO terms (functions) as the positive genes. In addition, we also collected genes that showed any potential association with AD from the above-described resources. These genes were then combined with the genes annotated to the GO terms, forming a set of genes of potential association with AD, denoted by GS. Next, the negative gene set was then calculated as GN = GA - GS, where GA represents all the genes in the network. By removing the 19471 genes identified in GS from GA (21122 genes), 1651 genes that were not associated with AD were identified and used as non-AD (negatives) genes. Table 1. Resources for compiling AD-associated genes. No. of Resources Genes Filtering Criteria genes PSEN2, HFE, NOS3, PLAU, CALHM1, A2M, PSEN1, OMIM3 All genes associated with AD 12 ADAM10, MPO, ABCA7, APOE, APP APOC1, BCL3, MS4A4A, FRMD4A, GAB2, MTHFD1L, CR1, EPHA1, CLU, PICALM, Genome-wide significant association DistiLD5 19 SORL1, CD33, ABCA7, with AD (p-value < 5.0×10-8) CEACAM16, GLIS3, CD2AP, SRRM4, BCHE, ZNF292 CLU, TNK1, APOE, SOAT1, PVRL2, TRAK2, CHRNB2, TFAM, CTSD, IL33, THRA, IL1RN, IL10, PICALM, STH, IL6, CD33, TFCP2, VLDLR, SORCS1, IL1B, GAB2, ABCA1, CTNNA3, APOC2, IL1A, BIN1, DAPK1, PON1, CST3, CCR2, The top ranked AD genes provided AlzGene11 GAPDHS, IL8, GRN, ECE1, 68 on the AlzGene website. OLR1, TF, LPL, LRP1, HHEX, GAPDH, LDLR, OTC, ARID5B, TNF, TOMM40, EXOC3L2, PGBD1, PRNP, BCAM, CALHM1, UBQLN1, PCK1, NEDD9, SORL1, ADAM10, MME, ENTPD7, FAS, CH25H, APOC1, ACE, CYP19A1, NCAPD2, MTHFR, APOC4, CHAT, CR1 APP, PSEN1, PSEN2, MAPT, APOE, TREM2, PLD3, SORL1, NOTCH3, CLU, PICALM, CR1, ABCA7, BIN1, CD33, CD2AP, MS4A6A, MS4A4E, NME8, Top ranked genes supported by AlzBase2 32 EPHA1, PTK2B, SLC24A4, genetic evidences CELF1, FERMT2, ZCWPW1, INPP5D, HLA-DRB1, HLA- DRB5, MEF2C, TP53INP1, CASS4, IGHV1-67 PSEN1, APP, PSEN2, APOE, Genes associated with AD and score DisGenet12 SORL1, MAPT, BDNF, IL1B, 12 > 0.3 BACE1, ACE, GSK3B, PLAU ADAM10, APOE, APP, MT-ND1, UniProt 6 MT-ND2, PSEN1, PSEN2, All genes associated with AD 8 SORL1 SLC30A6(ZNT6)13, 14, SLC30A4(ZNT4)13, 14, MAOB15, 16, CHRNA717, 18, IGF119, 20, VEGFA21, 22, ARC23, 24, PPARG25, 26, BCL227, 28, 29, IGF2R30, CASP331, 32, NECTIN2 (PVRL2)33, 34, 35, IGF230, 36, 37, VSNL138, 39, ACHE40, 41, 42, CYP46A143, 44, 45, IDE46, 47, 1. For GWAS studies: p- NPY48, 49, 50, IGF1R20, 51, value<5.0×10-8 Published PM20D152, APBB253, 54, ESR155, 2. For differential gene expression 56 literature 56, 57, PAXIP158, 59, CRH60, 61, studies on AD, the gene which is SOD262, 63, 64, SLC2A465, 66, differentially expressed in at least HMOX167, 68, DPYSL269, 70, two studies were included. INSR71, 72, DHCR2473, 74, 75, RELN76, 77, 78, 79, 80, BAX81, 82, 83, REST84, MEOX285, 86, EIF2AK387, 88, MAN2A189, 90, (ABI3, PLCG2)91, 92, DSG226, 93, MS4A294, 95,PPP1R3796, RELB33, 97, TREML298, (HESX1, ADAMTS4, CLNK, HS3ST1, CNTNAP2, ADAM10, APH1B, KAT8, ABI3, ALPK2, ECHDC3, SCIMP, SUZ12P1)99 p-value<5.0×10-8; from both GWAS- GWAS reported and GWAS-mapped genes 265 catalog https://www.ebi.ac.uk/gwas as provided in the GWAS catalog database. Open Genes with association score with AD 175 Targets7 https://www.opentargets.org/ > 0.5 ROSMAP See ref9 All DEGs with FDR<0.05 2614 Table 2. The list of 147 AD-associated genes. AD-associated genes APOE, SORL1, GAB2, CR1, PICALM, CLU, CD33, ABCA7, ADAM10, CD2AP, BIN1, APOC1, TOMM40, INPP5D, PSEN2, EPHA1, APP, MTHFD1L, CNTNAP2, HLA-DRB1, CASS4, BCAM, ABCA1, PTK2B, MS4A6A, FRMD4A, BCL3, SLC24A4, GLIS3, FERMT2, PSEN1, TREM2, ZCWPW1, EXOC3L2, MS4A4A, ACE, APOC4, BZW2, SUCLG2, APOB, SCIMP, SCARB1, RELB, CRY2, PVRL2, CLASRP, ADAMTS4, MMP3, UBE2L3, PPP1R37, ECHDC3, TCF7L2, IL6R, MS4A2, LIPG, MAN2A1, MAPT, ALDH1A2, ABI3, LILRA5, CELF1, PLCG2, HMGCR, OARD1, APH1B, APOC2, OR4S1, STAT4, MS4A4E, PVR, MT-ND2, HS3ST1, CCR2, VASP, CYP8B1, BLOC1S3, PPP1R13L, NFIC, NKPD1, INSR, CNTNAP5, BCAS3, BCHE, BCL2, NME8, CLPTM1, CLNK, UBQLN1, CLMN, IL1B, TRAPPC6A, VSNL1, SORCS1, PPARG, IGSF23, CRH, PSMA1, CHRNB2, FBXL7, CHRNA7, SPON1, MYO16, CHRNA2, VLDLR, KIR3DL2, KIT, HLA-DRB5, BACE1, HLA- DRA, DSG2, CALHM1, RBFOX1, HFE, PILRA, LRP4, HARBI1, TFCP2, CBLC, DPP10, SYNJ1, CDC25B, ACP2, ACHE, PACSIN3, MADD, ZNF652, GSK3B, PFDN1, RIN3, MARK4, GRIN2A, PDGFRB, MAPK8IP1, GRIN3B, CCRL2, ECE1, SCN1A, HBEGF, CACNA1G, CEACAM16, MMP13, ESR1, ALDH5A1, PLAU, SCN8A, CACNA2D1, MMP12 References 1. 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