Abstract 5132: Interactively exploring patterns in TCGA data: a web-based compendium of ‘next-generation’ clustered heat maps

Each of the 5 TCGA marker paper published in Nature to date has included at least one clustered heat map (CHM). We introduced CHMs in the early 1990’s for pharmacogenomic analysis (1) and later for integrated visualization of genomic, transcriptomic, proteomic, pharmacological, and functional data (1). As the ubiquitous first-order way of visualizing omic data, CHMs have appeared in many thousands of publications (3–9), including those from TCGA. We have elsewhere summarized their limitations (10). One such limitation is that CHMs are generally static images. We therefore initiated the next-generation CHM (NG-CHM) project, using an image-tiling technology similar to that in Google Maps for navigation and extreme drill-down without loss of resolution. Once the CHM has been zoomed sufficiently, labels (e.g., gene, protein, or drug names) appear on the image's axes. Clicking on a label produces a menu of link-outs (e.g., to GeneCards, Google, PubMed). For gene vs. gene maps, each pixel can represent a color-coded Pearson correlation coefficient. Clicking on the pixel pulls up the corresponding data scattergram, bootstrap statistics, literature references, or pathway relationships. Strong usability features include floating windows, flexible search tools, cluster selection tools, customizable re-coloring of the CHM, and high-quality PDF's suitable for publication. NG-CHMs are a major resource for exploratory analysis and visualization in multiple projects of TCGA and other large-scale molecular profiling programs. Explore interactive versions for TCGA breast, colorectal, lung squamous, and glioblastoma data at http://bioinformatics.mdanderson.org/main/TCGA/NGCHM. Supported in part by NCI Grant No. U24CA143883, by a gift from the Mary K. Chapman Foundation, and by a grant from the Michael and Susan Dell Foundation honoring Lorraine Dell. Citation Format: John N. Weinstein, David W. Kane, Rehan Akbani, Deepti Dodda, Lam Nguyen, Michael C. Ryan, Chris Wakefield, Bradley M. Broom. Interactively exploring patterns in TCGA data: a web-based compendium of ‘next-generation’ clustered heat maps. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5132. doi:10.1158/1538-7445.AM2013-5132