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. 2017 Nov 1;77(21):e23-e26.
doi: 10.1158/0008-5472.CAN-17-0318.

A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data

Bradley M Broom  1 , Michael C Ryan  2 , Robert E Brown  2 , Futa Ikeda  2 , Mark Stucky  2 , David W Kane  3 , James Melott  4 , Chris Wakefield  4 , Tod D Casasent  4 , Rehan Akbani  4 , John N Weinstein  1   5
Affiliations

A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data

Bradley M Broom et al. Cancer Res. .

Abstract

Clustered heatmaps are the most frequently used graphics for visualization of molecular profiling data in biology. However, they are generally rendered as static, or only modestly interactive, images. We have now used recent advances in web technologies to produce interactive "next-generation" clustered heatmaps (NG-CHM) that enable extreme zooming and navigation without loss of resolution. NG-CHMs also provide link-outs to additional information sources and include other features that facilitate deep exploration of the biology behind the image. Here, we describe an implementation of the NG-CHM system in the Galaxy bioinformatics platform. We illustrate the algorithm and available computational tool using RNA-seq data from The Cancer Genome Atlas program's Kidney Clear Cell Carcinoma project. Cancer Res; 77(21); e23-26. ©2017 AACR.

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Figures

Figure 1
Figure 1
Screenshots of the NG-CHM viewer. (a) Screenshot of the viewer showing RNAseq data from the TCGA project. The left-hand pane shows an overview of the entire heat map. The right-hand pane shows a zoomed view of the highlighted region. The location of the zoomed view is indicated in the left-hand pane by a green rectangle. The bar at the top contains interactive control elements, including controls for zooming, changing zoom mode, searching, generating a PDF, saving a local copy, and changing map options. (b) Context-specific menus which are displayed when the user right-clicks on a label. The top panel shows link-outs for TCGA sample identifiers, while the bottom panel shows link-outs for gene symbols. (c) Dialogue for re-coloring on the fly. The user can create a color map manually or choose a pre-defined color palette. The user can also choose the colors used for grid lines and the selection.
See this image and copyright information in PMC

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