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. 2024 Mar 20;15:2482. doi: 10.1038/s41467-024-46710-0

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© The Author(s) 2024

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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 6 — a Scaled expression of upregulated genes in each subclone in patient 022, showing genes in rows and subclones in columns. Genes in the COSMIC Cancer Gene Census³⁵ are highlighted. b UMAP embedding of expression profiles from patient 022 colored by clone labels assigned by integrated TreeAlign model. c Differentially expressed genes between clone A and other subclones (clone B-D) in patient 022. Adjusted P values were calculated by MAST³⁷. Proportions of subclonal differentially expressed genes located in CSCN regions for d 184-hTERT cell lines, e an HGSC control cell line and PDXs. f Pathways with clone-specific expression patterns in TNBC and HGSC PDXs. Source data are provided as a Source Data file.