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

. 2018 Dec 18;9:5368. doi: 10.1038/s41467-018-07806-6

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

© The Author(s) 2018

Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

PMC Copyright notice

Fig. 4 — The expression of only a small set of genes in T_reg cells is altered by low IL-2 signals: a 5 × 10⁴ T_reg and T_conv cells were sorted by flow cytometry from LNs of three independent replicate Il2ra^mut/mut or WT Foxp3^Rfp/Rfp reporter mice and total RNA extracted and reverse transcribed to cDNA. Affymetrix mouse expression arrays (Pico 1.0) were then conducted. Principal component analysis (PCA) of expressed genes using the top 10% of genes with the highest variance in analyzed groups with each symbol featuring one mouse. b Scatter plot of individual genes expressed in Il2ra^mut/mut vs WT T_reg cells. Significantly upregulated and downregulated genes, defined as genes with at least 1.5 fold change, p-value ≤ 0.01, are colored blue or black, respectively, and numbers are shown. c Heat map of selected genes grouped under various categories as indicated and for which expression is significantly different between Il2ra^mut/mut and WT T_reg cells. d Network analysis of biological-process gene-ontology (GO) term enrichment among significantly upregulated genes in Il2ra^mut/mut vs control WT T_reg cells. Upregulated genes were analyzed for over-represented GO terms using BiNGO in Cytoscape, and the resulting network was calculated and visualized using EnrichmentMap. Groups of similar GO terms were manually circled. Line thickness and color are proportional to the similarity coefficient between connected nodes. Node color is proportional to the FDR-adjusted p-value of the enrichment. Node size is proportional to gene set size. e Venn diagram comparing differentially expressed genes in Il2ra^mut/mut vs WT T_reg cells to genes with unique peaks called in Il2ra^mut/mut and WT T_reg cells found in ATAC-seq in Fig. 3 based on gene symbols. f ATAC-seq tracks for 3 sample genes with at least 1 unique peak localized in distinct regions of the gene (promotor, intronic, intergenic). g Three-way Venn diagram comparing differentially expressed genes in Il2ra^mut/mut versus WT T_reg cells to genes containing unique peaks close to TSS (<500 bp) in Il2ra^mut/mut vs WT T_reg cells found in ATAC-seq