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Next-Generation Clustered Heat Maps (NG-­CHM)

By Weinstein John1, Bradley Broom1

1. MD Anderson Cancer Center

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Clustered Heat Maps (CHMs) have been referred to as the ubiquitous visual icons of post-genomic biology -- the most frequent type of visualization for large molecular profiling databases. However, “traditional” CHMs are static images -- a serious limitation. Accordingly, we have now developed an interactive CHM-based environment for deep exploration of patterns in omic data – “Next-Generation” CHMs (NG-CHMs) in which one can zoom and navigate as in a Google map, link out to a variety of external information sources, invoke a statistical toolbox, change color schemes on the fly, save all metadata needed to reproduce the map months or years later, and produce high-resolution, publication-ready images. We propose to mature and harden that development (Aim #1), adding more toolbox features, increasing user- friendliness, increasing shearability, fleshing out an NG-CHM builder with 4 levels of sophistication for different degrees of expertise (Aim #2), and refining the visualizations to fit the needs of non-specialist cancer biologists and clinical researchers. We have also formed working relationships for linking NG- CHMs with other strong bioinformatics resources (Aim #3), including cBio, the UCSC Genome Browser and Cancer Genome Browser, Regulome Explorer, and TCPA and TANRIC, as well as “home-grown” developments like SpliceSeq and Mbatch. Analogous linkage can be developed with other ITCR software. We also propose to develop additional NG-CHM compendia for TCGA and ICGC (Aim #4) and to interact extensively with the cancer and bioinformatics communities by providing training through a combination of comprehensive written documentation, tutorial videos, webinars, workshops, and formats for obtaining feedback (Aim #5).


Mervi Heiskanen

National Cancer Institute