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 Aug 19;12:5045. doi: 10.1038/s41467-021-25188-0

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

© The Author(s) 2021

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 — NanoString gene expression analysis was performed in tumor-free nodes from patients with NIF (n = 8) and No-NIF (n = 29). The NIF group for these analyses includes patients with available nodal samples after neoadjuvant therapy that were cancer-free and contained non-caseating granulomas with available nodal NanoString expression data. a–f Violin plots show the distribution of immune scores (log₂ normalized counts) in nodes resected from NIF and No-NIF patients in the NEOSTAR study: immune cells expressing CD45 (a), macrophages (b), dendritic cells (DCs) (c), cytotoxic cells (d), Th1 cells (e), and exhausted CD8 T cells (f). The log₂ normalized counts are presented as median with minima, lower and upper quartiles, and maxima. The dashed line indicates the median; the dotted lines indicate the lower quartile and upper quartile values; top and bottom of the violin plots indicate the maxima and minima. The red circles depict data from NIF group, and the blue squares depict data from No-NIF group. g Differential expression of genes between NIF and No-NIF nodal samples are illustrated as a volcano plot. Red dots depict significantly upregulated genes in NIF compared to No-NIF nodes and blue dots represent significantly upregulated genes in nodes of No-NIF compared to nodes of NIF patients. h Bar plots showing differentially expressed pathways between nodes of NIF and No-NIF patients, computed by GSEA analysis. Red bars indicate pathways that are upregulated while blue bars indicate pathways that are downregulated in nodes of NIF compared to nodes of No-NIF patients. Two-sided P value is from Wilcoxon rank-sum test in panels (a–f). Two-sided P values are from Welch’s t-test in panel (g). P values (FDR-adjusted < 0.2) are from GSEA algorithm in panel (h). NIF, nodal immune flare; DCs, dendritic cells; Th1, T helper cells 1. NES, normalized enrichment score. Source data are provided as a Source Data file and Supplementary Data file (Supplementary Data 1).