Abstract 2979: A web portal of ‘next-generation’ clustered heat maps for user-friendly, interactive exploration of patterns in TCGA data (2015)

Abstract The Cancer Genome Atlas (TCGA) program is generating comprehensive molecular profiles of more than 30 clinical tumor types, the first 12 of which have been incorporated into a “Pan-Cancer12” project. One bioinformatic challenge is statistical analysis of the resulting profiles; a second is the visual detective work necessary to explore individual genes, pathways and patterns in the data. For that type of detective work, we introduced CHMs in the early 1990s for pharmacogenomic analysis (1) and later for integrated visualization of genomic, transcriptomic, proteomic, pharmacological, and functional data (2). As the ubiquitous first-order way of visualizing omic data, CHMs have appeared in many thousands of publications (3-9), including all of the major publications by the TCGA Research Network. However, a major limitation is that they have been static or only modestly interactive graphics. We have now developed “next-generation” clustered heat maps (NG-CHMs), which use a Google-maps-like tiling technology for extreme zooming and navigation without loss of resolution. NG-CHMs provide pathway and gene ontology information, re-coloring on the fly, tools for reproducibility, high-resolution graphics output, a statistical toolbox, and link-outs to public sources of information on genes, proteins, pathways and drugs. The result is a visually rich, dynamic environment for exploration of the masses of data produced by TCGA. The compendium of TCGA Pan-Cancer NG-CHMs currently includes 667 maps as an initial set, but the numbers will soon rise into the thousands as more data types, tumour types and algorithms are incorporated (at web portal http://bioinformatics.mdanderson.org/TCGA/NGCHMPortal/). As an illustrative example, NG-CHMs proved pivotal as a tool for discovering and analyzing molecular target themes common to multiple types of gynecological cancers and themes that distinguish them from each other. 1. Weinstein JN … Paull KD. Stem Cells 12; 13, 1994. 2. Weinstein JN … Paull KD. Science 275;343, 1997. 3. Myers TG … Weinstein JN. Electrophoresis 18; 467, 1997. 4. Eisen MB … Botstein D. Proc. Natl. Acad. Sci. U.S.A. 14863, 1998. 5. Golub TR … Lander ES. Science 286; 531, 1999. 6. Ross DT … Brown PA. Nature Genetics 24; 227, 2000 7. Scherf U … Weinstein JN. Nature Genetics 24; 236, 2000. 8. Zeeberg BR … Weinstein JN. BMC Bioinformatics 6; 168, 2005. 9. Weinstein JN. Science 319; 1772, 2008. 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. Note: This abstract was not presented at the meeting. Citation Format: John N. Weinstein, Rehan Akbani, David W. Kane, James M. Melott, Tod D. Casasent, Rong Yao, Paul L. Roebuck, Gordon B. Mills, Michael C. Ryan, Christopher Wakefield, Bradley M. Broom. A web portal of ‘next-generation’ clustered heat maps for user-friendly, interactive exploration of patterns in TCGA data. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2979. doi:10.1158/1538-7445.AM2015-2979