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

. 2021 Oct;31(10):1885–1899. doi: 10.1101/gr.271080.120

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

© 2021 Wang et al.; Published by Cold Spring Harbor Laboratory Press

This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

PMC Copyright notice

Figure 2. — Transcriptional activator and repressor classification. (A) Volcano plot of differentially expressed TF genes between the HC and PC/DC clusters (P-adjusted < 0.05). (B) UMAP of TF motif accessibility z-scores calculated from chromVAR. Cells are color-coded based on SnapATAC clusters. (C) Volcano plot of differential TF motif accessibilities calculated from z-scores between the HC and PC/DC clusters (P-adjusted < 0.05). (D) Dot plot of TF classification shown in average log₂ fold change (FC) mRNA level and z-scores. The differential expression from scRNA-seq between HCs and PC/DCs is plotted on the x-axis, and the differential accessibility from scATAC-seq is shown on the y-axis. Activators are classified in green, repressors in red, and undetermined TFs in gray. (E–H) TF activities in differentiating HCs and PC/DCs in terms of mRNA expression, chromatin accessibility, and footprints. (E) LHX3, a transcriptional activator in HCs. (First row) Violin plot of RNA expression. Each dot represents a single cell. (Second row) UMAP plot of LHX3 motif accessibility calculated as z-score. Red indicates higher accessibility compared with blue. Each dot represents a single cell. (Third row) LHX3 footprint calculated from scATAC-seq data using HINT-ATAC. Activators are characterized by high scATAC-seq signal in the flanking region of the TF binding sites compared with the control population. Yellow line represents the HC cluster, and orange line represents the PC/DC cluster. (Fourth row) Mouse HOCOMOCO v10 consensus sequence for the LHX3 motif. (F–H) Analogous data representation for (F) GFI1, classified as a HC repressor; (G) SOX2, a PC/DC activator; and (H) TGIF1, a repressor in PC/DCs.