Fig. 5
Top piggyBac CIS genes are recurrently altered in human brain gliomas. a Patient data was analyzed from The Cancer Genome Atlas (TCGA) datasets (n = 283 LGGs, 273 GBMs; LGG data shown here, GBM data shown in Additional file 1: Fig. S24), for cross-comparison of the main CIS genes in mouse brain and spinal tumors. The frequency of alterations of CIS genes observed in patient samples is indicated. Similar genes (NF1 and SPRED1) and co-deleted/co-amplified genes have been grouped together. TCF12 and SPRED1 are co-deleted (chromosome 15q), as are QKI, UST, PPP1R14C, and MAP7 (chromosome 6p), as well as EXOSC9 and CLCN3 (chromosome 4q). ASAP1 and CSMD3 (chromosome 8q) are co-amplified in human tumors. From these 20 top CIS genes, there are 28 gene pairs with significantly co-occurring alterations in human LGGs, many of which are on neighboring chromosomal locations; 8 pairs had mutually exclusive alterations (Bonferroni-corrected p value < 0.05, Fisher’s exact test); for simplicity, only the key co-occurring alterations are highlighted here. b–e Kaplan-Meier plots of GBM patient survival in relation to expression levels of key mutated novel genes SOX6 (b), UST (c), and TCF12 (d) in TCGA and REMBRANDT (e–g) datasets. P values were calculated using the log-rank test comparing the top 30% of expression level with the lower 70% for each gene. All survival data from TCGA and REMBRANDT GBM datasets were used (n = 348 and n = 329 patients respectively with survival data), to ensure a sufficient sample size; analyses were performed using the open web interface “Project Betastasis” (www.betastasis.com)