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. 2022 Aug 6;13:4594. doi: 10.1038/s41467-022-32283-3

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© The Author(s) 2022

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/.

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Fig. 7 — a Heatmap showing seven tumor microenvironment (TME) subtypes of HCC patients (TME1–7) with distinct composition of immune and stromal cell subtypes inferred from bulk RNA-seq data of the TCGA-LIHC cohort. Rows represent the 29 patient-shared immune and stromal cell subtypes identified by the scRNA-seq data in this study. Columns represent the 369 HCC patients from the TCGA-LIHC cohort. Tumor-node-metastasis (TNM) stages, etiology, PanImmune subtypes and iCluster subtypes are annotated by colors at the top of the heatmap. b Kaplan–Meier survival analysis shows that the seven TME subtypes exhibit distinct overall survival outcomes. The statistical significance was determined by log-rank test. c The distribution of the normalized abundances of representative cell subtypes (VEGFA⁺ and MMP9⁺ TAMs, top; CTLs and Tregs, bottom) between TME subtypes TME2 (n = 50 patients) versus TME5 (n = 25 patients), and TME3 (n = 45 patients) versus TME7 (n = 69 patients), respectively. In set boxplot elements are defined in the Methods section (section on data visualization). The statistical significances were determined by two-sided Student’s t test. CTL cytotoxic T lymphocytes, TAM tumor-associated macrophage, Treg regulatory T cell. Source data are provided as a Source Data file.