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

. 2020 May 5;217(7):e20191369. doi: 10.1084/jem.20191369

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

© 2020 Santos et al.

This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.rupress.org/terms/). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 4.0 International license, as described at https://creativecommons.org/licenses/by-nc-sa/4.0/).

PMC Copyright notice

Figure 8. — Differential expression and gene enrichment pathway analysis in circulating lymphocytes. (A and B) Volcano plots show differential gene expression by fold change (logFC) and P value (−log10[p]) for the PanCancer Immune Profiling and CAR-T Characterization NanoString gene panels comparing good (SD/PR) with bad (PD) outcome groups at baseline (d0; A) and d43 (B) in circulating lymphocyte samples. Table S3 lists information about the samples selected for NanoString profiling. Dark blue dots denote nonsignificant genes, purple dots denote significant genes with fold change ≤1.85, light blue dots represent genes with fold change ≥1.85 and P value ≥0.05, and red dots indicate genes with fold change ≥1.85 and P value ≤0.05. Summary of pathways identified by GSEA/MSigDB analysis as showing enrichment among highly differentially expressed genes at d0 (A) and d43 (B). The y axis denotes NES, and the squares represent up-regulated (red, associated with good outcome) and down-regulated (blue, associated with bad outcome) pathways with corresponding gene enrichment P values indicated on the midline. (C) GSEA plot for the CTLA-4 inhibitory pathway and a heatmap of its associated gene set, illustrating enrichment for down-regulation at d43 relative to d0. (D) GSEA plot for the PD-1 signaling pathway and its associated gene set, which is down-regulated at d89 versus d43 in circulating lymphocytes. For C and D, circulating lymphocytes from patients with good clinical outcome were used, as there were no available samples from PD patients. Heatmaps in C and D show the clustered genes in the leading-edge subsets for each pathway category. Gene expression values are represented as colors, where the range of colors (red, pink, light blue, dark blue) shows the range of expression values (high, moderate, low, lowest).