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. 2022 May 10;13:2558. doi: 10.1038/s41467-022-30050-y

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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. 2 — Oncoprints of recurrently mutated genes, excluding IG and chromosome Y genes (a). Mutated genes are listed from top to bottom depending on their alteration frequency. The corresponding dot plot reflects the log2 fold change and significance of alteration frequencies in the other subcohorts and RNAseq subgroups compared to PCNSL. The recurrently mutated genes (listed in the oncoprint in a) were analyzed by Metascape⁶⁸ to identify pathway and process enrichment (b) and transcriptional regulatory networks (TRRUST) (c). Metascape adopts the hypergeometric test and employs the Benjamini-Hochberg correction for multiple testing. Oncoprints of driver genes in PCNSL (d). The top panel of the oncoprint shows the total numbers of structural variants (SVs), small insertions/deletions (INDELs), single nucleotide variants (SNVs), estimated ploidy, and genomic tumor cell content (TCC). Mutated genes are ranked by IntOGen. The corresponding dot plot reflects the log2 fold change and significance of alteration frequencies in the other subcohorts and RNAseq subgroups compared to PCNSL. In panels (a) and (d) the size of the dots demonstrate the significance according to a two-tailed Fisher’s exact test not corrected for multiple testing.