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. 2024 Feb 7;25:45. doi: 10.1186/s13059-024-03172-3

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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/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 4 — A Network plots showing the GBM biology-specific gene sets (described in Additional file 1: Table S24) that are significantly enriched (FDR < 0.05) in either, or both, Up or Down responders through treatment. Large gray hub nodes indicate the gene sets. These have associated, smaller, leaf nodes signifying the genes in that set, colored according to the strength and direction of differential expression through treatment (quantified as -log₁₀p-value multiplied by the direction of fold change: -log10(pval)direction) in Up responders (left image) or Down responders (right image). B As for panel C but visualizing the Hallmark gene sets from MSigDB that were enriched with an FDR < 0.25 in either, or both, responder subtypes. C The proportion of neural stem cell markers of quiescence (qNSC) or active cycling (aNSC), or markers of more differentiated neuroblasts (NB) or oligodendrocytes (Oligo), that were upregulated (yellow), downregulated (green), or stable (blue) in Up (left) and Down (right) responders