About

In Noori et al. (2020), we performed a systematic review and meta-analysis of human CNS transcriptomic datasets in the public Gene Expression Omnibus (GEO) and ArrayExpress repositories across Alzheimer's disease (AD), Lewy body diseases (LBD), and the amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD) disease spectrum. Here, we provide the source code to generate the data quality reports and perform differential expression analyses for these datasets. Please see our accompanying publication in Data In Brief for additional information.

Prerequisites

Please install R to run our code, as well as all requisite packages.

Vignette

Our vignette is available at www.ayushnoori.com/nd-diff-expr.

Citations

Research Paper: Noori, A.,^1,2,3,4, Mezlini, A.M.,^2,3,4,5, Hyman, B.T.,^2,4,5, Serrano-Pozo, A.,^2,4,5*, Das, S.^2,3,4,5. (2021). Systematic review and meta-analysis of human transcriptomics reveals neuroinflammation, deficient energy metabolism, and proteostasis failure across neurodegeneration. Neurobiology of Disease, 149, 105225. doi: 10.1016/j.nbd.2020.105225.

Methods Paper: Noori, A.,^1,2,3,4, Mezlini, A.M.,^2,3,4,5, Hyman, B.T.,^2,4,5, Serrano-Pozo, A.,^2,4,5*, Das, S.^2,3,4,5. (2021). Central nervous system differential gene expression data across Alzheimer’s disease, Lewy body diseases, and ALS-FTD. Data in Brief, 35, 106863. doi: 10.1016/j.dib.2021.106863.

Affiliations

1. Harvard College, Cambridge, MA 02138, United States of America
2. Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, United States of America
3. MIND Data Science Lab, Cambridge, MA 02139, United States of America
4. MassGeneral Institute for Neurodegenerative Disease, Charlestown, MA 02129, United States of America
5. Harvard Medical School, Boston, MA 02115, United States of America

* Co-Corresponding Authors

Acknowledgements

This work was supported by the Alzheimer’s Association (AACF-17-524184 to AS-P), the National Institute on Aging (K08AG064039 to AS-P and P30AG062421 to BTH and SD), the Rainwater Charitable Foundation (to BTH), and a MassLife Sciences MassCATS award (to BTH and SD). The funding sources had no role in study design; data collection, analysis and interpretation; or manuscript preparation.