TABLE 1.
List of brain transcriptomic datasets used for obtaining aging and AD gene signatures.
| Datasets | Gene list ID | List details (tissue, traits) | # of genes (UP/DOWN) | # of protein coding genes | Sample size |
| GTEx “aging” sets (age ≤ 70) | |||||
| GTEx | G_AMY | Amygdala | 50(19/31) | 46(19/27) | 46 |
| GTEx | G _BA24_AC | Anterior_cingulate_cortex (BA24) | 1460(473/987) | 1208(320/888) | 56 |
| GTEx | G_CAU | Caudate (basal_ganglia) | 77(50/27) | 55(34/21) | 75 |
| GTEx | G_CRBH | Cerebellar_Hemisphere | 322(138/184) | 277(108/169) | 73 |
| GTEx | G_CRBL | Cerebellum | 427(213/214) | 340(162/178) | 87 |
| GTEx | G_CTX | Cortex | 97(34/63) | 78(30/48) | 71 |
| GTEx | G_BA9 DLPFC | Frontal_Cortex (BA9) | 15(8/7) | 12(5/7) | 61 |
| GTEx | G_HIPP | Hippocampus | 1804(950/854) | 1403(705/698) | 57 |
| GTEx | G_HYPO | Hypothalamus | 2140(822/1318) | 1650(490/1160) | 53 |
| GTEx | G_NC | Nucleus_accumbens (basal_ganglia) | 11(6/5) | 9(5/4) | 69 |
| GTEx | G_PUTM | Putamen (basal_ganglia) | 18(13/5) | 17(13/4) | 67 |
| UK “aging” sets (age ≤ 70) | |||||
| UK | UK_FCTX | Frontal cortex (FCTX) | 170(50/120) | 145(42/103) | 94 |
| UK | UK_TCTX | Temporal cortex (TCTX) | 678(169/509) | 510(91/419) | 82 |
| UK | UK_OCTX | Occipital cortex (OCTX) | 54(30/24) | 44(23/21) | 95 |
| UK | UK_WHMT | Intralobular white matter (WHMT) | 464(267/197) | 373(204/169) | 93 |
| UK | UK_CRBL | Cerebellum (CRBL) | 186(101/85) | 156(87/69) | 92 |
| UK | UK_PUTM | Putamen (PUTM) | 65(30/35) | 52(22/30) | 95 |
| UK | UK_THAL | Thalamus (THAL) | 12(8/4) | 9(5/4) | 91 |
| UK | UK_HIPP | Hippocampus (HIPP) | 959(544/415) | 755(431/324) | 93 |
| Other “AD” sets | |||||
| MSSM | MSSM_FP | BM10(MSSM_FP) | 54(20/34) | 47(19/28) | 135 |
| MSSM | MSSM_IFG | BM44(MSSM_IFG) | 71(24/47) | 61(24/37) | 116 |
| MSSM | MSSM_PHG | BM36(MSSM_PHG) | 1577(936/641) | 1391(868/523) | 103 |
| MSSM | MSSM_STG | BM22(MSSM_STG) | 269(150/119) | 242(142/100) | 122 |
| Mayo | Mayo_CRBL_Source* | Cerebellum | 2632(1360/1272) | 2282(1231/1051) | 151 |
| Mayo | Mayo_CRBL | Cerebellum | 1880(1008/872) | 1600(901/699) | 151 |
| Mayo | Mayo_TCTX_Source* | Temporal cortex | 3842(2034/1808) | 3437(1933/1504) | 151 |
| Mayo | Mayo_TCTX | Temporal cortex | 2951(1663/1288) | 2628(1578/1050) | 151 |
| ROSMAP | ROSMAP_DLPFC | Dorsolateral prefrontal cortex (DLPFC) | 162(89/73) | 141(80/61) | 241 |
| Annese2018 | Annese2018_HIPP | Hippocampus | 2122(808/1314) | 1925(742/1183) | 10 |
| Rooij2019 | Rooij2019_HIPP | Hippocampus | 2840(1109/1731) | 2667(1045/1622) | 28 |
| Jager | Jager_Clinical_AD | Clinical_AD in DLPFC | 855(466/389) | 740(412/328) | 478 |
| Jager | Jager_Cognitive_decline | Cognitive_decline in DLPFC | 3035(1481/1554) | 2662(1281/1381) | 478 |
| Jager | Jager_Tau_tangles | Tau_tangles in DLPFC | 238(155/83) | 209(133/76) | 478 |
| Jager | Jager_B_amyloid | B_amyloid in DLPFC | 2315(1158/1157) | 2020(1060/960) | 478 |
| Jager | Jager_Patho_AD | Patho_AD in DLPFC | 98(58/40) | 85(51/34) | 478 |
| MS “AD” sets | |||||
| MS | MS_BM10_FP | Frontal pole | 19(5/14) | 17(5/12) | 63 |
| MS | MS_BM17_OCTX | Occipital visual cortex | 345(325/21) | 297(279/19) | 53 |
| MS | MS_BM20_ITG | Inferior temporal gyrus | 397(397/0) | 349(349/0) | 58 |
| MS | MS_BM21_MTG | Middle temporal gyrus | 635(81/565) | 571(66/516) | 58 |
| MS | MS_BM22_STG | Superior temporal gyrus | 25(0/25) | 24(0/24) | 60 |
| MS | MS_BM23_PCC | Posterior cingulate cortex | 34(7/27) | 29(7/22) | 58 |
| MS | MS_BM32_AC | Anterior cingulate | 239(33/207) | 214(30/184) | 59 |
| MS | MS_BM36_PHG | Parahippocampal gyrus | 55(7/49) | 48(6/42) | 60 |
| MS | MS_BM38_TP | Temporal pole | 44(28/16) | 39(25/14) | 58 |
| MS | MS_BM4_PCG | Precentral gyrus | 131(8/123) | 122(7/115) | 49 |
| MS | MS_BM44_IFG | Inferior frontal gyrus | 874(589/566) | 764(513/495) | 53 |
| MS | MS_BM46_DLPFC | Dorsolateral prefrontal cortex | 58(11/47) | 53(8/45) | 57 |
| MS | MS_BM7_SPL | Superior parietal lobule | 346(240/110) | 314(220/97) | 50 |
| MS | MS_BM8_SFG | Superior prefrontal gyrus | 953(426/670) | 869(386/617) | 56 |
| MS | MS_CD | Caudate nucleus | 31(30/1) | 29(28/1) | 52 |
| MS | MS_HIPP | Hippocampus | 107(25/82) | 95(22/73) | 55 |
| MS | MS_PUTM | Putamen | 94(52/42) | 82(45/37) | 52 |
*AMP-AD Mayo gene signature is based on SourceDiagnosis.