Department of Bioinformatics and Computational Biology

Home > Public Software > NG-CHM > TCGA Supplements > CRC

Next Generation Clustered Heat Maps for TCGA Colon and Rectal Cancer (CRC) paper

This page contains links to Next Generation Clustered Heat Maps (NG-CHM) to supplement the TCGA colon and rectal cancer paper . 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 .

NGCHM similar to figure 5 of the CRC paper

We currently provide a heatmap similar to figure 5 of the paper, in two versions. The first is best viewed on a high resolution monitor, the second is more suitable for viewing on laptops and other resolution challenged interfaces.

CRC heatmap, large, CRC heatmap, small

 (Please try again shortly if the server is unresponsive due to exceptionally high demand.)

The data matrix contained in the heatmap above contains the same data that was used in the paper. The auxiliary information (such as classification bars) may be updated.

NGCHM showing gene-gene correlations

This NGCHM shows the correlations between all pairs of genes for 500 of the most highly variable genes in this dataset. An alternative view shows the gene pairs for which there is evidence of an interaction, with linkouts (where applicable) to publications in pubmed that provide evidence supporting the interaction.

CRC Gene-Gene heatmap.

NGCHM Sample Sample Distance

This CHM displays the distances between samples, based on the expression levels for the 500 most highly variable genes in this dataset. The primary data layer shows the bootstrapped cosine distance. The second data layer (click Switch Data) shows the Pearson correlation.

CRC Sample-Sample heatmap.

Future Plans

We also plan to provide further auxiliary information and other related heatmaps in the near future. 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.


Special thanks to Josh Stuart for providing the data on which this NG-CHM is based.

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.