Association As. 2012 Alzheimer’s disease facts and figures. Alzheimers Dement. 2012;8(2):131–68.

Article  Google Scholar 

Long JM, Holtzman DM. Alzheimer disease: an update on pathobiology and treatment strategies. Cell. 2019;179(2):312–39.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hampel H, Frank R, Broich K, Teipel SJ, Katz RG, Hardy J, et al. Biomarkers for Alzheimer's disease: academic, industry and regulatory perspectives. Nat Rev Drug Discov. 2010;9(7):560–74.

Article  CAS  PubMed  Google Scholar 

Kou X, Chen D, Chen N. The regulation of microRNAs in Alzheimer's disease. Front Neurol. 2020;11:288.

Article  PubMed  PubMed Central  Google Scholar 

Wang M, Qin L, Tang B. MicroRNAs in Alzheimer’s disease. Front Genet. 2019;10:153.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Patrick E, Rajagopal S, Wong H-KA, McCabe C, Xu J, Tang A, et al. Dissecting the role of non-coding RNAs in the accumulation of amyloid and tau neuropathologies in Alzheimer’s disease. Mol Neurodegener. 2017;12(1):1–13.

Article  Google Scholar 

Winter J, Jung S, Keller S, Gregory RI, Diederichs S. Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol. 2009;11(3):228–34.

Article  CAS  PubMed  Google Scholar 

Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. cell. 2004;116(2):281–97.

Article  CAS  PubMed  Google Scholar 

Arora T, Prashar V, Singh R, Barwal TS, Changotra H, Sharma A, et al. Dysregulated miRNAs in progression and pathogenesis of Alzheimer’s disease. Mol Neurobiol. 2022;59(10):1–18.

Miya Shaik M, Tamargo IA, Abubakar MB, Kamal MA, Greig NH, Gan SH. The role of microRNAs in Alzheimer’s disease and their therapeutic potentials. Genes. 2018;9(4):174.

Article  PubMed  PubMed Central  Google Scholar 

Lau P, Frigerio CS, De Strooper B. Variance in the identification of microRNAs deregulated in Alzheimer's disease and possible role of lincRNAs in the pathology: the need of larger datasets. Ageing Res Rev. 2014;17:43–53.

Article  CAS  PubMed  Google Scholar 

Carter SL, Brechbühler CM, Griffin M, Bond AT. Gene co-expression network topology provides a framework for molecular characterization of cellular state. Bioinformatics. 2004;20(14):2242–50.

Article  CAS  PubMed  Google Scholar 

Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A. 1998;95(25):14863–8.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9(1):1–13.

Article  Google Scholar 

Pedersen HK, Forslund SK, Gudmundsdottir V, Petersen AØ, Hildebrand F, Hyötyläinen T, et al. A computational framework to integrate high-throughput ‘-omics’ datasets for the identification of potential mechanistic links. Nat Protoc. 2018;13(12):2781–800.

Article  CAS  PubMed  Google Scholar 

Zhang T, Shen Y, Guo Y, Yao J. Identification of key transcriptome biomarkers based on a vital gene module associated with pathological changes in Alzheimer’s disease. Aging (Albany NY). 2021;13(11):14940.

Article  CAS  PubMed  Google Scholar 

Bennett DA, Schneider JA, Aggarwal NT, Arvanitakis Z, Shah RC, Kelly JF, et al. Decision rules guiding the clinical diagnosis of Alzheimer’s disease in two community-based cohort studies compared to standard practice in a clinic-based cohort study. Neuroepidemiology. 2006;27(3):169–76.

Article  PubMed  Google Scholar 

Bennett D, Schneider J, Arvanitakis Z, Kelly J, Aggarwal N, Shah R, et al. Neuropathology of older persons without cognitive impairment from two community-based studies. Neurology. 2006;66(12):1837–44.

Article  CAS  PubMed  Google Scholar 

Braak H, Alafuzoff I, Arzberger T, Kretzschmar H, Del Tredici K. Staging of Alzheimer disease-associated neurofibrillary pathology using paraffin sections and immunocytochemistry. Acta Neuropathol. 2006;112(4):389–404.

Article  PubMed  PubMed Central  Google Scholar 

Mirra SS, Heyman A, McKeel D, Sumi S, Crain BJ, Brownlee L, et al. The Consortium to Establish a Registry for Alzheimer's Disease (CERAD): part II. Standardization of the neuropathologic assessment of Alzheimer's disease. Neurology. 1991;41(4):479–9.

Article  CAS  PubMed  Google Scholar 

Wan Y-W, Al-Ouran R, Mangleburg CG, Perumal TM, Lee TV, Allison K, et al. Meta-analysis of the Alzheimer’s disease human brain transcriptome and functional dissection in mouse models. Cell Rep. 2020;32(2):107908.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Henriques AD, Machado-Silva W, Leite RE, Suemoto CK, Leite KR, Srougi M, et al. Genome-wide profiling and predicted significance of post-mortem brain microRNA in Alzheimer’s disease. Mech Ageing Dev. 2020;191:111352.

Article  CAS  PubMed  Google Scholar 

Kozomara A, Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014;42(D1):D68–73.

Article  CAS  PubMed  Google Scholar 

De Jager PL, Ma Y, McCabe C, Xu J, Vardarajan BN, Felsky D, et al. A multi-omic atlas of the human frontal cortex for aging and Alzheimer’s disease research. Sci Data. 2018;5(1):1–13.

Article  Google Scholar 

Zhang Y, Parmigiani G, Johnson WE. ComBat-seq: batch effect adjustment for RNA-seq count data. Genom Bioinform. 2020;2(3):lqaa078.

Article  Google Scholar 

Karpenko O, Bahroos N, Chukhman M, Dong X, Kanabar P, Arbieva Z, et al. Galaxy high throughput genotyping pipeline for GeneTitan. AMIA Jt Summits Transl Sci Proc. 2013;2013:102–2.

PubMed  Google Scholar 

Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003;4(2):249–64.

Article  PubMed  Google Scholar 

Ringnér M. What is principal component analysis? Nat Biotechnol. 2008;26(3):303–4.

Article  PubMed  Google Scholar 

Wang M, Beckmann ND, Roussos P, Wang E, Zhou X, Wang Q, et al. The Mount Sinai cohort of large-scale genomic, transcriptomic and proteomic data in Alzheimer's disease. Sci Data. 2018;5(1):1–16.

Article  Google Scholar 

Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7(3):562–78.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10(3):1–10.

Article  Google Scholar 

Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics. 2011;12:1–16.

Article  Google Scholar 

Yang H-S, White CC, Klein H-U, Yu L, Gaiteri C, Ma Y, et al. Genetics of gene expression in the aging human brain reveal TDP-43 proteinopathy pathophysiology. Neuron. 2020;107(3):496–508.e496.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bennett D, Schneider J, Bienias J, Evans D, Wilson R. Mild cognitive impairment is related to Alzheimer disease pathology and cerebral infarctions. Neurology. 2005;64(5):834–41.

Article  CAS  PubMed  Google Scholar 

Schneider JA, Arvanitakis Z, Bang W, Bennett DA. Mixed brain pathologies account for most dementia cases in community-dwelling older persons. Neurology. 2007;69(24):2197–204.

Article  PubMed  Google Scholar 

Wilson RS, Segawa E, Boyle PA, Anagnos SE, Hizel LP, Bennett DA. The natural history of cognitive decline in Alzheimer's disease. Psychol Aging. 2012;27(4):1008.

Article  PubMed  PubMed Central  Google Scholar 

Nam J-W, Rissland OS, Koppstein D, Abreu-Goodger C, Jan CH, Agarwal V, et al. Global analyses of the effect of different cellular contexts on microRNA targeting. Mol Cell. 2014;53(6):1031–43.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wong N, Wang X. miRDB: an online resource for microRNA target prediction and functional annotations. Nucleic Acids Res. 2015;43(D1):D146–52.

Article  CAS  PubMed  Google Scholar 

Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44–57.

Article  CAS  PubMed  Google Scholar