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MS Margaretha A. Skowron
MV Marieke Vermeulen
AW Anna Winkelhausen
TB Teresa K. Becker
FB Felix Bremmer
PP Patrick Petzsch
SS Stefan Schönberger
GC Gabriele Calaminus
KK Karl Köhrer
PA Peter Albers
DN Daniel Nettersheim
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Venn diagrams were generated using Venny 2.1 (https://bioinfogp.cnb.csic.es/tools/venny/).31 The STRING algorithm was used to predict interactive networks from RNA-seq data (https://string-db.org).32 Functional annotation analyses were performed by DAVID (https://david.ncifcrf.gov/home.jsp).33,34 In functional annotation analyses of commonly deregulated genes in GCT cells, only categories (UP_Keywords) with at least five members and p values ≤0.05 were considered significant. For functional annotation analysis of genes deregulated in each GCT cell line, only categories (UP_Keywords) with at least ten members and a p value ≤0.05 was considered significant. Only genes related to an official human gene symbol were included. ‘The Cancer Genome Atlas’ (TCGA) datasets were analysed for isoform/gene expression, DNA methylation and copy number alterations (CNAs) using the UCSC Xena browser (https://xena.ucsc.edu) and the cBioPortal (https://www.cbioportal.org).35–37

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