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. 2018 Mar 29;8:5351. doi: 10.1038/s41598-018-21937-2

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© 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/.

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Healthy livers are a critical reference group for identifying differentially regulated immune cell types and pathways in HCC. (A) A gene set enrichment analysis was performed to detect coordinated changes of gene expression in gene sets of immune cell type-specific marker genes. Three inter-group comparisons were performed (HCC-T vs. HCC-NT; HCC-T vs. HL; HCC-NT vs. HL). Colour intensity reflects the log₁₀ transformed p-value from the enrichment analysis. Magenta colour indicates higher expression compared to the reference group while cyan colour indicates weaker expression compared to the reference group. (B,C) Selected immune pathways from an IPA^® on the three major inter-group comparisons (B) activated pathways shared by HCC-T and HCC-NT; (C) pathways activated in either HCC-T or HCC-NT).