Department of Bioinformatics and Computational Biology

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Next Generation Clustered Heat Maps for TCGA LUSC

This page will contain links to Next Generation Clustered Heat Maps (NG-CHM) related to TCGA data for LUSC. NG-CHM are highly interactive, dynamic clustered heatmaps that enable the user to see an overview of the entire heatmap, and via interactive navigation controls, to zoom and pan across the heatmap to see details of the heatmap at many levels of resolution. Other interactive controls enable searching for specific heatmap entries, generating production quality PDFs, and linking out to information related to rows, columns, and individual heatmap entries. The user interface is mostly intuitive, although a few less commonly used features can only be accessed with the use of specific keys. These are documented in the Viewer user manual. Before using TCGA data, please read TCGA guidelines for publication and moratoriums .


We currently provide a gene by sample heatmap of the mRNA data.

mRNA Gene by Sample

Future Plans

We plan to make NG-CHM based on TCGA LUSC data publically available on publication of the applicable TCGA paper. These may include NG-CHM similar to the static figures in the paper, as well as additional NG-CHM related to the LUSC data. Please contact John Weinstein or Bradley Broom if there is a specific feature or heatmap you would like to see.

More Information and other TCGA Datasets

More information about the NGCHM tool and its application to TCGA datasets is available at the TCGA NGCHM page.


The NG-CHM tool was developed by the MDACC Genome Data Analysis Center (GDAC) led by John Weinstein. Major contributors to the tool’s design and development include David Kane, Bradley Broom, Deepti Dodda, Lam Nguyen, Sid Acharya, Panna Shetty, Rehan Akbani, Chris Wakefield, and Allen Chang.

Supported by Grant Number U24CA143883 from the National Cancer Institute. Also supported in part by a gift from the H.A. & Mary K. Chapman Foundation and a grant from the Michael & Susan Dell Foundation.