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. 2020 Apr 7;11:1723. doi: 10.1038/s41467-020-15283-z

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© The Author(s) 2020

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 Heat map of the 4609 proteins that passed through quality filters in TMT-Integrator for all samples (3 MMTV-cre;Ccn6^fl/fl mouse tumors (KO) and 3 normal mouse mammary glands). Scale bar shows expression level (red is upregulated and green is downregulated). b Volcano plot comparing Ccn6^fl/fl tumors with normal mammary gland. Significantly differentially expressed proteins are highlighted in red. p < 0.05 and absolute value FC > 1 were considered significant. c Gene set enrichment analysis (GSEA) showing significant differentially expressed protein pathways in Ccn6^fl/fl spindle MBCs compared with normal mammary glands. Normalized enrichment scores (NES) versus the total list of GSEA hallmark categories of up and downregulated hallmark pathways. d Top hallmark pathways highlighting significantly expressed up- and downregulated protein pathways (marked UP and DOWN, respectively). We used the molecular Signatures Database (MSigDB v7.0), hallmark gene sets with clusterProfiler and fgsea packages in R, with the biomaRT package in R to convert mouse gene IDs to human homolog associated gene symbols. e Venn diagrams demonstrate the overlap between the proteome of mouse MBC and human spindle MBC tumors, relative to their normal tissue counterparts, identifying a 17-protein upregulated and 19-protein downregulated protein set. Protein–protein interaction networks of up- and downregulated signatures highlight potential markers of interest, along with functional enrichment analysis using STRING v11.0. Color scheme of network proteins are matched by the legend of GO enrichment terms in barplots.