CEP-IP with CMRF in SEA-AD Microglia: A Mitochondrial Co-expression Module Linked to Cognition

CEP-IP with CMRF in SEA-AD Microglia: A Mitochondrial Co-expression Module Linked to Cognition (Supplementary Methods, Supplementary Figures S1-S21, and Supplementary Tables S1-S19) [Preprint on bioRxiv] Author: Kah Keng WongPreprint: bioRxiv (2026)DOI: 10.5281/zenodo.23445742 Abstract Background: Single-nucleus RNA-seq (snRNA-seq) studies of Alzheimer’s disease (AD) routinely filter nuclei by mitochondrial percentage (%MT) or remove mitochondrial genes, yet whether these reads carry information about cognition is rarely examined. Methods: In the SEA-AD microglia snRNA-seq dataset, a transcriptome-wide screen identified a module of MT-CO3 and eight co-expressed mitochondrial genes. Three microglial populations were analyzed: M4 (Mic.13-like), PVM_3, and PVM_1, with a housekeeping-gene control in M4 cells. The CEP-IP pipeline with a copula monotone recovery filter (CMRF) used per-cell Spearman and Kendall scores, an inflection point (IP), and a cross-validated copula space boundary to isolate MT-CO3 Module cells. Results: The donor percentage of Module cells past the IP (Module post-IP%) was significantly associated with worse cognition (MMSE and CASI; FDR<0.05) in all three populations. In M4 and PVM_3, these associations remained significant after adjustment for tissue quality, plaque burden, tangle burden, and contamination, and after doublet removal. M4 and PVM_3 Module post-IP% repeated in each donor’s regions beyond chance, and no per-cell %MT cutoff reproduced the Module cells. However, at the donor level, Module post-IP% could not be separated from mean %MT, and the source of the mitochondrial transcripts (e.g., retained cytoplasm or a true change in mitochondrial content) remains unresolved. Conclusions: Routine %MT filtering in AD snRNA-seq may therefore remove cells that carry information about cognition. The full pipeline code, software container, processed data, and the R package cepip are publicly available, and reruns of the full pipeline in the container reproduced the original findings. Description This record provides the Supplementary Methods (PDF), Supplementary Figures S1-S21 (PDF), and Supplementary Tables S1-S19 (Excel format) for "CEP-IP with CMRF in SEA-AD Microglia: A Mitochondrial Co-expression Module Linked to Cognition" by Kah Keng Wong, preprint on bioRxiv (2026). The supplementary tables include: Cell Selection, GOI-DFG Screens, and Pre-checks (Supplementary Tables S1-S6) Cell-level Scores, Inflection Points, Copula Coordinates, and CMRF (Supplementary Tables S7-S10) Differential Expression and Clinical Association (Supplementary Tables S11-S12) Batteries 1 to 5 (Supplementary Tables S13-S17) M4 against PVM_3 and Summary of All Tests (Supplementary Tables S18-S19) Citation If using these figures and tables, please cite:Wong KK. CEP-IP with CMRF in SEA-AD Microglia: A Mitochondrial Co-expression Module Linked to Cognition. bioRxiv (2026). Wong KK. CEP-IP: An explainable framework for cell subpopulation identification in single-cell transcriptomics. Computer Methods and Programs in Biomedicine, 282 (2026) 109372.https://doi.org/10.1016/j.cmpb.2026.109372 Also cite the source datasets:M.I. Gabitto, K.J. Travaglini, V.M. Rachleff, E.S. Kaplan, B. Long, et al. Integrated multimodal cell atlas of Alzheimer's disease. Nature Neuroscience, 27 (2024) 2366-2383.https://doi.org/10.1038/s41593-024-01774-5 K.J. Travaglini, M.I. Gabitto, Y. Ding, A. Agrawal, N. Postupna, et al. Multiregional single-cell profiling reveals shared and specialized cellular vulnerability in Alzheimer's disease. bioRxiv (2026).https://www.biorxiv.org/content/10.64898/2026.07.01.734821v1 E. Gerrits, N. Brouwer, S.M. Kooistra, M.E. Woodbury, Y. Vermeiren, et al. Distinct amyloid-beta and tau-associated microglia profiles in Alzheimer's disease. Acta Neuropathologica, 141 (2021) 681-696.https://doi.org/10.1007/s00401-021-02263-w License The figures and tables are licensed under the Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0). They are derived from the Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) of the Allen Institute for Brain Science, and their use is subject to the Allen Institute Terms of Use (noncommercial research use) and Citation Policy. Commercial use needs the written permission of the Allen Institute. Related Resources Preprint: bioRxiv (2026) Processed dataset: Hugging Face: kahkengwong/CEP-IP_with_CMRF_in_SEA-AD Code: GitHub: kahkengwong/CEP-IP_with_CMRF_in_SEA-AD CEP-IP framework: Computer Methods and Programs in Biomedicine, 282 (2026) 109372 Source datasets: SEA-AD portal; GEO: GSE148822 R package: GitHub: kahkengwong/cepip