Supplementary Table 1. The list of 1,675 all stages of AD-related upregulated genes Gene ID Gene symbol Gene name 51146 A4GNT ALPHA-1,4-N-ACETYLGLUCOSAMINYLTRANSFERASE 9625 AATK APOPTOSIS-ASSOCIATED TYROSINE KINASE 19 ABCA1 ATP-BINDING CASSETTE, SUB-FAMILY A (ABC1), MEMBER 1 20 ABCA2 ATP-BINDING CASSETTE, SUB-FAMILY A (ABC1), MEMBER 2 10058 ABCB6 ATP-BINDING CASSETTE, SUB-FAMILY B (MDR/TAP), MEMBER 6 89845 ABCC10 ATP-BINDING CASSETTE, SUB-FAMILY C (CFTR/MRP), MEMBER 10 5826 ABCD4 ATP-BINDING CASSETTE, SUB-FAMILY D (ALD), MEMBER 4 25 ABL1 V-ABL ABELSON MURINE LEUKEMIA VIRAL ONCOGENE HOMOLOG 1 3983 ABLIM1 ACTIN BINDING LIM PROTEIN 1 30 ACAA1 ACETYL-COENZYME A ACYLTRANSFERASE 1 (PEROXISOMAL 3-OXOACYL-COENZYME A THIOLASE) 35 ACADS ACYL-COENZYME A DEHYDROGENASE, C-2 TO C-3 SHORT CHAIN 8310 ACOX3 ACYL-COENZYME A OXIDASE 3, PRISTANOYL 56 ACRV1 ACROSOMAL VESICLE PROTEIN 1 2180 ACSL1 ACYL-COA SYNTHETASE LONG-CHAIN FAMILY MEMBER 1 86 ACTL6A ACTIN-LIKE 6A 93973 ACTR8 ACTIN-RELATED PROTEIN 8 91 ACVR1B ACTIVIN A RECEPTOR, TYPE IB 8747 ADAM21 ADAM METALLOPEPTIDASE DOMAIN 21 27299 ADAMDEC1 ADAM-LIKE, DECYSIN 1 56999 ADAMTS9 ADAM METALLOPEPTIDASE WITH THROMBOSPONDIN TYPE 1 MOTIF, 9 105 ADARB2 ADENOSINE DEAMINASE, RNA-SPECIFIC, B2 (RED2 HOMOLOG RAT) 109 ADCY3 ADENYLATE CYCLASE 3 113 ADCY7 ADENYLATE CYCLASE 7 120 ADD3 ADDUCIN 3 (GAMMA) 125 ADH1C ALCOHOL DEHYDROGENASE 1A (CLASS I), ALPHA POLYPEPTIDE 9370 ADIPOQ ADIPONECTIN, C1Q AND COLLAGEN DOMAIN CONTAINING 165 AEBP1 AE BINDING PROTEIN 1 4299 AFF1 AF4/FMR2 FAMILY, MEMBER 1 173 AFM AFAMIN 79814 AGMAT AGMATINE UREOHYDROLASE (AGMATINASE) 10555 AGPAT2 1-ACYLGLYCEROL-3-PHOSPHATE O-ACYLTRANSFERASE 2 (LYSOPHOSPHATIDIC ACID ACYLTRANSFERASE, BETA) 375790 AGRN AGRIN 185 AGTR1 ANGIOTENSIN II RECEPTOR, TYPE 1 187 AGTRL1 ANGIOTENSIN II RECEPTOR-LIKE 1 25909 AHCTF1 AT HOOK CONTAINING TRANSCRIPTION FACTOR 1 202 AIM1 ABSENT IN MELANOMA 1 203 AK1 ADENYLATE KINASE 1 204 AK2 ADENYLATE KINASE 2 8165 AKAP1 A KINASE (PRKA) ANCHOR PROTEIN 1 11214 AKAP13 LYMPHOID BLAST CRISIS ONCOGENE 10270 AKAP8 A KINASE (PRKA) ANCHOR PROTEIN 8 26993 AKAP8L A KINASE (PRKA) ANCHOR PROTEIN 8-LIKE 10142 AKAP9 A KINASE (PRKA) ANCHOR PROTEIN (YOTIAO) 9 1645 AKR1C1 ALDO-KETO REDUCTASE FAMILY 1, MEMBER C1 (DIHYDRODIOL DEHYDROGENASE 1; 20-ALPHA (3-ALPHA)- HYDROXYSTEROID DEHYDROGENASE) 8644 AKR1C3 ALDO-KETO REDUCTASE FAMILY 1, MEMBER C3 (3-ALPHA HYDROXYSTEROID DEHYDROGENASE, TYPE II) 10000 AKT3 V-AKT MURINE THYMOMA VIRAL ONCOGENE HOMOLOG 3 (PROTEIN KINASE B, GAMMA) 8854 ALDH1A2 ALDEHYDE DEHYDROGENASE 1 FAMILY, MEMBER A2 224 ALDH3A2 ALDEHYDE DEHYDROGENASE 3 FAMILY, MEMBER A2 7840 ALMS1 ALSTROM SYNDROME 1 51421 AMOTL2 ANGIOMOTIN LIKE 2 272 AMPD3 ADENOSINE MONOPHOSPHATE DEAMINASE (ISOFORM E) 29882 ANAPC2 ANAPHASE PROMOTING COMPLEX SUBUNIT 2 284 ANGPT1 ANGIOPOIETIN 1 23452 ANGPTL2 ANGIOPOIETIN-LIKE 2 10541 ANP32B ACIDIC (LEUCINE-RICH) NUCLEAR PHOSPHOPROTEIN 32 FAMILY, MEMBER B 301 ANXA1 ANNEXIN A1 302 ANXA2 ANNEXIN A2 314 AOC2 AMINE OXIDASE, COPPER CONTAINING 2 (RETINA-SPECIFIC) 162 AP1B1 ADAPTOR-RELATED PROTEIN COMPLEX 1, BETA 1 SUBUNIT 10239 AP3S2 ADAPTOR-RELATED PROTEIN COMPLEX 3, SIGMA 2 SUBUNIT 9546 APBA3 AMYLOID BETA (A4) PRECURSOR PROTEIN-BINDING, FAMILY A, MEMBER 3 (X11-LIKE 2) 339 APOBEC1 APOLIPOPROTEIN B MRNA EDITING ENZYME, CATALYTIC POLYPEPTIDE 1 341 APOC1 APOLIPOPROTEIN C-I 346 APOC4 APOLIPOPROTEIN C-IV 23780 APOL2 APOLIPOPROTEIN L, 2 54840 APTX APRATAXIN 358 AQP1 AQUAPORIN 1 (COLTON BLOOD GROUP) 363 AQP6 AQUAPORIN 6, KIDNEY SPECIFIC 8260 ARD1A ARD1 HOMOLOG A, N-ACETYLTRANSFERASE (S. CEREVISIAE) 382 ARF6 ADP-RIBOSYLATION FACTOR 6 55738 ARFGAP1 ADP-RIBOSYLATION FACTOR GTPASE ACTIVATING PROTEIN 1 384 ARG2 ARGINASE, TYPE II 392 ARHGAP1 RHO GTPASE ACTIVATING PROTEIN 1 55114 ARHGAP17 RHO GTPASE ACTIVATING PROTEIN 17 23092 ARHGAP26 RHO GTPASE ACTIVATING PROTEIN 26 395 ARHGAP6 RHO GTPASE ACTIVATING PROTEIN 6 9639 ARHGEF10 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR (GEF) 10 22899 ARHGEF15 RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR (GEF) 15 27237 ARHGEF16 RHO GUANINE EXCHANGE FACTOR (GEF) 16 23370 ARHGEF18 RHO/RAC GUANINE NUCLEOTIDE EXCHANGE FACTOR (GEF) 18 8289 ARID1A AT RICH INTERACTIVE DOMAIN 1A (SWI- LIKE) 5926 ARID4A AT RICH INTERACTIVE DOMAIN 4A (RBP1-LIKE) 51742 ARID4B AT RICH INTERACTIVE DOMAIN 4B (RBP1- LIKE) 25852 ARMC8 ARMADILLO REPEAT CONTAINING 8 10095 ARPC1B ACTIN RELATED PROTEIN 2/3 COMPLEX, SUBUNIT 1B, 41KDA 51593 ARS2 ARS2 PROTEIN 51665 ASB1 ANKYRIN REPEAT AND SOCS BOX-CONTAINING 1 140462 ASB9 ANKYRIN REPEAT AND SOCS BOX-CONTAINING 9 429 ASCL1 ACHAETE-SCUTE COMPLEX-LIKE 1 (DROSOPHILA) 22809 ATF5 ACTIVATING TRANSCRIPTION FACTOR 5 64422 ATG3 ATG3 AUTOPHAGY RELATED 3 HOMOLOG (S. CEREVISIAE) 23192 ATG4B ATG4 AUTOPHAGY RELATED 4 HOMOLOG B (S. CEREVISIAE) 57205 ATP10D ATPASE, CLASS V, TYPE 10D 8992 ATP6V0E1 ATPASE, H+ TRANSPORTING, LYSOSOMAL 9KDA, V0 SUBUNIT E 538 ATP7A ATPASE, CU++ TRANSPORTING, ALPHA POLYPEPTIDE (MENKES SYNDROME) 5205 ATP8B1 ATPASE, CLASS I, TYPE 8B, MEMBER 1 57099 AVEN APOPTOSIS, CASPASE ACTIVATION INHIBITOR 552 AVPR1A ARGININE VASOPRESSIN RECEPTOR 1A 563 AZGP1 ALPHA-2-GLYCOPROTEIN 1, ZINC 8704 B4GALT2 UDP-GAL:BETAGLCNAC BETA 1,4- GALACTOSYLTRANSFERASE, POLYPEPTIDE 2 60468 BACH2 BTB AND CNC HOMOLOGY 1, BASIC LEUCINE ZIPPER TRANSCRIPTION FACTOR 2 572 BAD BCL2-ANTAGONIST OF CELL DEATH 573 BAG1 BCL2-ASSOCIATED ATHANOGENE 54971 BANP BTG3 ASSOCIATED NUCLEAR PROTEIN 11177 BAZ1A BROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN, 1A 11176 BAZ2A BROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN, 2A 29994 BAZ2B DKFZP434H071 PROTEIN 4059 BCAM BASAL CELL ADHESION MOLECULE (LUTHERAN BLOOD GROUP) 587 BCAT2 BRANCHED CHAIN AMINOTRANSFERASE 2, MITOCHONDRIAL 596 BCL2 B-CELL CLL/LYMPHOMA 2 604 BCL6 B-CELL CLL/LYMPHOMA 6 (ZINC FINGER PROTEIN 51) 605 BCL7A B-CELL CLL/LYMPHOMA 7A 7439 BEST1 VITELLIFORM MACULAR DYSTROPHY 2 (BEST DISEASE, BESTROPHIN) 51283 BFAR BIFUNCTIONAL APOPTOSIS REGULATOR 632 BGLAP BONE GAMMA-CARBOXYGLUTAMATE (GLA) PROTEIN 633 BGN BIGLYCAN 23743 BHMT2 BETAINE-HOMOCYSTEINE METHYLTRANSFERASE 2 274 BIN1 BRIDGING INTEGRATOR 1 55909 BIN3 BRIDGING INTEGRATOR 3 329 BIRC2 BACULOVIRAL IAP REPEAT-CONTAINING 2 27302 BMP10 BONE MORPHOGENETIC PROTEIN 10 55589 BMP2K BMP2 INDUCIBLE KINASE 657 BMPR1A BONE MORPHOGENETIC PROTEIN RECEPTOR, TYPE IA 8315 BRAP BRCA1 ASSOCIATED PROTEIN 672 BRCA1 BREAST CANCER 1, EARLY ONSET 23774 BRD1 BROMODOMAIN CONTAINING 1 6046 BRD2 BROMODOMAIN CONTAINING 2 8019 BRD3 BROMODOMAIN CONTAINING 3 23476 BRD4 BROMODOMAIN CONTAINING 4 7862 BRPF1 BROMODOMAIN AND PHD FINGER CONTAINING, 1 680 BRS3 BOMBESIN-LIKE RECEPTOR 3 7832 BTG2 BTG FAMILY, MEMBER 2 10950 BTG3 BTG FAMILY, MEMBER 3 10384 BTN3A3 BUTYROPHILIN, SUBFAMILY 3, MEMBER A3 10917 BTNL3 BUTYROPHILIN-LIKE 3 8945 BTRC BETA-TRANSDUCIN REPEAT CONTAINING 745 C11ORF9 CHROMOSOME 11 OPEN READING FRAME 9 57102 C12ORF4 CHROMOSOME 12 OPEN READING FRAME 4 56905 C15ORF39 CHROMOSOME 15 OPEN READING FRAME 39 8131 C16ORF35 CHROMOSOME 16 OPEN READING FRAME 35 115939 C16ORF42 CHROMOSOME 16 OPEN READING FRAME 42 29965 C16ORF5 CHROMOSOME 16 OPEN READING FRAME 5 753 C18ORF1 CHROMOSOME 18 OPEN READING FRAME 1 51029 C1ORF121 CHROMOSOME 1 OPEN READING FRAME 121 81627 C1ORF25 CHROMOSOME 1 OPEN READING FRAME 25 715 C1R COMPLEMENT COMPONENT 1, R SUBCOMPONENT 716 C1S COMPLEMENT COMPONENT 1, S SUBCOMPONENT 27296 C20ORF10 CHROMOSOME 20 OPEN READING FRAME 10 51526 C20ORF111 CHROMOSOME 20 OPEN READING FRAME 111 79144 C20ORF149 CHROMOSOME 20 OPEN READING FRAME 149 55257 C20ORF20 CHROMOSOME 20 OPEN READING FRAME 20 55317 C20ORF29 CHROMOSOME 20 OPEN READING FRAME 29 25980 C20ORF4 CHROMOSOME 20 OPEN READING FRAME 4 755 C21ORF2 CHROMOSOME 21 OPEN READING FRAME 2 56245 C21ORF62 CHROMOSOME 21 OPEN READING FRAME 62 54149 C21ORF91 CHROMOSOME 21 OPEN READING FRAME 91 6936 C2ORF3 CHROMOSOME 2 OPEN READING FRAME 3 51161 C3ORF18 CHROMOSOME 3 OPEN READING FRAME 18 56941 C3ORF37 CHROMOSOME 3 OPEN READING FRAME 37 23272 C3ORF63 CHROMOSOME 3 OPEN READING FRAME 63 721 C4B COMPLEMENT COMPONENT 4B (CHIDO BLOOD GROUP) 8603 C4ORF8 CHROMOSOME 4 OPEN READING FRAME 8 727 C5 COMPLEMENT COMPONENT 5 10826 C5ORF4 CHROMOSOME 5 OPEN READING FRAME 4 730 C7 COMPLEMENT COMPONENT 7 84909 C9ORF3 CHROMOSOME 9 OPEN READING FRAME 3 90477 C9ORF33 CHROMOSOME 9 OPEN READING FRAME 33 9413 C9ORF61 CHROMOSOME 9 OPEN READING FRAME 61 11094 C9ORF7 CHROMOSOME 9 OPEN READING FRAME 7 759 CA1 CARBONIC ANHYDRASE I 56997 CABC1 CHAPERONE, ABC1 ACTIVITY OF BC1 COMPLEX LIKE (S. POMBE) 773 CACNA1A CALCIUM CHANNEL, VOLTAGE-DEPENDENT, P/Q TYPE, ALPHA 1A SUBUNIT 8913 CACNA1G CALCIUM CHANNEL, VOLTAGE-DEPENDENT, ALPHA 1G SUBUNIT 800 CALD1 CALDESMON 1 91860 CALML4 CALMODULIN-LIKE 4 124583 CANT1 CALCIUM ACTIVATED NUCLEOTIDASE 1 825 CAPN3 CALPAIN 3, (P94) 10498 CARM1 COACTIVATOR-ASSOCIATED ARGININE METHYLTRANSFERASE 1 22794 CASC3 CANCER SUSCEPTIBILITY CANDIDATE 3 8573 CASK CALCIUM/CALMODULIN-DEPENDENT SERINE PROTEIN KINASE (MAGUK FAMILY) 57513 CASKIN2 CASK INTERACTING PROTEIN 2 836 CASP3 CASPASE 3, APOPTOSIS-RELATED CYSTEINE PEPTIDASE 837 CASP4 CASPASE 4, APOPTOSIS-RELATED CYSTEINE PEPTIDASE 839 CASP6 CASPASE 6, APOPTOSIS-RELATED CYSTEINE PEPTIDASE 842 CASP9 CASPASE 9, APOPTOSIS-RELATED CYSTEINE PEPTIDASE 831 CAST CALPASTATIN 865 CBFB CORE-BINDING FACTOR, BETA SUBUNIT 868 CBLB CAS-BR-M (MURINE) ECOTROPIC RETROVIRAL TRANSFORMING SEQUENCE B 28952 CCDC22 COILED-COIL DOMAIN CONTAINING 22 29080 CCDC59 COILED-COIL DOMAIN CONTAINING 59 26112 CCDC69 COILED-COIL DOMAIN CONTAINING 69 26093 CCDC9 COILED-COIL DOMAIN CONTAINING 9 54535 CCHCR1 COILED-COIL ALPHA-HELICAL ROD PROTEIN 1 896 CCND3 CYCLIN D3 10983 CCNI CYCLIN I 2826 CCR10 CHEMOKINE (C-C MOTIF) RECEPTOR 10 25819 CCRN4L