Gene Set Enrichment Analysis of DAPK1 Knockout

Pre-ranked GSEA was performed using the GSEA V3.0 software^{24 (link),25 (link)} using standard settings and all gene sets included in the Molecular Signatures Database v6.2. As input we used expression fold change values (DAPK1 ko clones vs. HCT116) for the 770 transcripts profiled by the nCounter^® PanCancer Progression Panel (NanoString Technologies Hamburg, Germany). Gene sets were manually categorized into functional gene-set groups representing biological properties relevant to this paper using the following keywords for each category: ECM matrix (keywords: matrisome, ECM, extracellular collagen); EMT/invasion (keywords: mesenchymal, invasive, epithelial cell migration); integrin pathways (keyword: integrin); cell-substrate adhesion (keywords: matrix adhesion, substrate adhesion, focal adhesion); and healing/inflammation (keywords: wound, “inflam”); Cell–cell adhesion (keywords: cell cycle); chromosome organization (keywords: chromosome, chromatin). All gene sets containing the terms “positive regulation of”, “Negative regulation of”, “UP” and “DN” were omitted from the analysis.

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Steinmann S., Kunze P., Hampel C., Eckstein M., Bertram Bramsen J., Muenzner J.K., Carlé B., Ndreshkjana B., Kemenes S., Gasparini P., Friedrich O., Andersen C., Geppert C., Wang S., Eyupoglu I., Bäuerle T., Hartmann A, & Schneider-Stock R. (2019). DAPK1 loss triggers tumor invasion in colorectal tumor cells. Cell Death & Disease, 10(12), 895.

Publication 2019

nCounter® PanCancer Progression Panel

Biological Cell adhesion Cell cycle Cell migration Chromatin Chromosome Chromosome organization Clones Collagen Focal adhesion Gene Inflammation Integrin Mesenchymal Progression Wound

Corresponding Organization :

Other organizations : Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg, Aarhus University Hospital, The Ohio State University

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Variable analysis

independent variables

DAPK1 ko clones vs. HCT116

dependent variables

Expression fold change values for the 770 transcripts profiled by the nCounter® PanCancer Progression Panel

control variables

Standard settings of the GSEA V3.0 software
All gene sets included in the Molecular Signatures Database v6.2

controls

No positive or negative controls were explicitly mentioned in the provided input.

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