Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2022 Mar 2;17:17. doi: 10.1186/s13024-022-00517-z

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2022

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

PMC Copyright notice

Fig. 3 — Recommended workflow of feature selection, dimension reduction, and clustering, and applications in AD. A Recommended workflow of dimension reduction and unsupervised clustering analysis of AD scRNA-seq data. Software tools are provided for each step. B Technical variance vs biological variance plot from the ROSMAP snRNA-seq data. The red dots depict genes with significantly greater biological variance than the technical variance (FDR < 0.05) and the top 20 most significant genes are labeled. C PC versus percentage of the variance explained. Vertical lines indicate recommended number of PCs from different workflows (red: PC denoising workflow from scran, blue: elbow point from Seurat, green: default number of PCs in Seurat). D UMAP plot of snRNA-seq from ROSMAP cohort. Clustering by PhenoGraph implemented in Seurat is marked by numeric labels. The cell types identified by marker gene expressions in (E) are highlighted as different border colors with relevant cell type name labels (Ast: astrocyte; End, endothelial; Ex: excitatory neurons; In: inhibitory neurons; Mic, microglia; Oli, oligodendrocytes; Opc: oligodendrocytes progenitor cells), and AD pathology (Healthy - green, early AD – yellow, late AD - red) are highlighted as different point colors. E dot plots of brain cell type markers showing their cluster-wise expressions. Clusters on the y-axis are ordered according to their proximity in the UMAP plot in (D). F Proportions of cells at different AD stages. FET is performed to evaluate whether the cells from each AD stage are enriched in each cell cluster. As significant enrichment is based on a cutoff of 0.05 for corrected FET p-value. In the plot, red dots represent the cases with fold enrichment (FE) > 1.3