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. 2023 Jul 11;11:113. doi: 10.1186/s40478-023-01610-0

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© The Author(s) 2023

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. 3 — Functional analysis of the RNA sequencing results (a) Top 20 terms of gene set enrichment analysis on gene ontology terms (chordoma I–chordoma C comparison) (b) Differentially expressed genes and terms from gene set enrichment analysis. Due to number of terms and genes top hits, basing on p-value, were selected (c) Weighted gene co-expression network analysis, presented on heatmap; samples are shown in columns, WGCNA modules in rows, significance of tests is shown in the panel on the left (d) WGCNA module 3 (with significantly higher score for chordoma I samples) intersected with STRING database; genes to plot were selected based on top connectivity (importance for the module) and centrality (best connected within module); gene names in bold were also differentially expressed in chordoma I, compared with chordoma C (e) Analogous for module 2, higher in chordoma versus nucleus pulposus, DEGs for chordoma—NP comparison are shown in bold