Fig. 4
TBX2 controls a FOXM1/E2F gene regulatory network. a Top enriched MsigDB hallmark genesets among the downregulated genes upon shTBX2 in IMR-5/75 (FD < 0.01) and the upregulated genes (FDR < 0.01) upon shTBX2 in IMR-5/75. Normalized enrichment score (NES) and false discovery rate (FDR) is depicted on the barcode plot. b iRegulon motif search for the downregulated and upregulated genes (FDR < 0.01) upon TBX2 knockdown in IMR-5/75. Genes connected to a gene in a white circle do have a motif enrichment or ChIP-seq binding for the respective gene in the circle. c GSEA results for genesets from literature (FOXM1 and E2F targets, and the downregulated genes upon CCND1 and CDK4 knockdown) which are enriched in the TBX2 downregulated genes in IMR-5/75. Normalized enrichment score (NES) and false discovery rate (FDR) is depicted on the barcode plot. d Western blot of TBX2, MYCN, and FOXM1 levels upon TBX2 knockdown, in the CLBGA MYCN single copy and IMR-5/75 MYCN amplified cell lines. e Clustering of genesets (MsigDB c5.bp.v4.0) correlated with TBX2 expression levels in the NRC tumor cohort (n = 283, GSE85047). Red nodes represent the gene sets positively correlated with TBX2 expression (FDR < 0.01, R > 4), blue nodes represent gene sets negatively correlated with TBX2 expression (FDR < 0.01, R < −0.3). Size of nodes depicts the size of the gene sets. Nodes that are clustered represent gene sets with the same or similar functional indication
