Department of Bioinformatics and Computational Biology

TCGA/NGCHM

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Contents

Next Generation Clustered Heat Maps for TCGA

The MD Anderson Genome Data Analysis Center


This page contains links to Next Generation Clustered Heat Maps (NG-CHM) to supplement a number of TCGA papers. 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.

Specific NGCHM pages

We have organized the NGCHM based on the disease and/or paper concerned, as detailed by the following table:

Paper / Disease NGCHM Page
Pan-Cancer 12 Compendium http://bioinformatics.mdanderson.org/TCGA/NGCHMPortal
Breast invasive carcinoma TCGA/Supplements/NGCHM-BRCA
Colorectal TCGA/Supplements/NGCHM-CRC
Glioblastoma TCGA/Supplements/NGCHM-GBM
Lung squamous cell carcinoma TCGA/Supplements/NGCHM-LUSC

Acknowledgements

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 Bradley Broom, David Kane, Michael Ryan, 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.