Superenhancers near the KLF5 gene are focally amplified in diverse cancer types. Superenhancers near the KLF5 gene are focally amplified in diverse cancer.

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Superenhancers near the KLF5 gene are focally amplified in diverse cancer types. Superenhancers near the KLF5 gene are focally amplified in diverse cancer types. A, Copy-number profile of the 13q22.1 noncoding region from HNSC, CESC, LUSC, ESCA, BLCA, STAD, and CRC. The copy-number peak, defined by statistical analysis with GISTIC (2, 109), in HNSC is highlighted. Color code is based on lineage types: squamous cell carcinomas, blue; urothelial carcinomas, green; adenocarcinomas, orange. B, DNA rearrangement analysis of the amplified noncoding region, using whole-genome sequencing data of head and neck squamous carcinoma samples from TCGA and the LUMPY program (37), demonstrates tandem duplications, as indicated by the curves. C, The merged ChIP-seq signal of the enhancer marker H3K27ac from cell lines representing HNSC, ESCA, and STAD. Superenhancers, indicated by thin bars, are called by the ROSE pipeline (39–41) based on the H3K27ac signal enrichment. BLCA, bladder carcinoma; CESC, cervical squamous cell carcinoma; CRC, colorectal adenocarcinoma; ESCA, esophageal carcinoma; GISTIC, genomic identification of significant targets in cancer; STAD, stomach adenocarcinoma; TCGA, The Cancer Genome Atlas. Xiaoyang Zhang et al. Cancer Discov 2018;8:108-125 ©2018 by American Association for Cancer Research