Existing Next-Generation Clustered Heat Maps (NG-CHMs)

View NG-CHMs Collections

This following list contains sites known to include NG-CHMs. The description for each site includes a link to the site and a brief guide to accessing the site’s NG-CHMs.

MD Anderson TCGA NG-CHM Compendium

We created a compendium of 297 interactive Next-Generation Clustered Heat Maps (NG-CHMs) for exploring cancer bioinformatics using data from the The Cancer Genome Atlas (TCGA) project.

The Cancer Genome Atlas (TCGA) NG-CHM Compendium

If you wish to preview details about each of the TCGA Maps in the compendium you can view detailed information about each map at this website

mSigDB/GSEA

The Molecular Signatures Database (MSigDB ) can generate dynamically an NG-CHM for a pathway and an expression profile.

• Select a pathway page (for instance (for instance the BIOCARTA_AKT_PATHWAY ).
• Goto the Compendia Expression Profiles entry and click on one of the expression profile links under NG-CHM interactive heatmaps.
• It can take several seconds for the heatmap to generate.

TCPA

The Cancer Proteome Atlas (TCPA) uses NG-CHMs for its heatmap visualizations. To access the heat maps:

• Select the Visualization button.
• Select Heatmap Visualizations.
• Select a dataset.
• Click on one of the heatmap thumbnails.

cBioPortal

For cBioPortal studies for which we have related NG-CHMs, the cBioPortal page for that study will include a “Heatmaps” tab.

For example, the TCGA Prostate Cancer page on cBioPortal includes such a tab.

• Click on the tab to show a matrix of related NG-CHMs.
• Click on a thumbnail to open the corresponding NG-CHM.

MBatch Omic Browser

The MBatch Omic Browser (MQA) provides an interface to evaluate batch effects in data from the Genome Data Commons (GDC). NG-CHMs are one of the visualizations provided by MQA. To view an NG-CHM:

• Select a Program from the drop down list (for example, TCGA).
• While additional drop down lists appear (these are program specific), choose an entry from the list until you are down to a single matching dataset. (For TCGA, you can try Project: TCGA-BRCA, Category: RNA-Seq, Details: RNASeq-FPKM, DataSet Type: Original, Results Version: 2022_12_28_1300.)
• The Visualization page for the selected dataset should be displayed.
• Select NGCHM from the Algorithm dropdown in the left column. Large NG-CHMs may take a while to download.

MetaBatch Omic Browser

The MetaBatch Omic Browser (MOB) provides an interface to evaluate batch effects in data from the Metabolomics Workbench. NG-CHMs are one of the visualizations provided by MOB. To view an NG-CHM:

• Select a Study ID from the drop down list (for example, ST000045).
• If an Analysis ID drop down is then displayed, select one. (If you picked study ST000045, try AN000072.)
• The Visualization page for the selected study and analysis, if applicable, should be displayed.
• Select NGCHM from the Algorithm dropdown in the left column. Large NG-CHMs may take a while to download.

TANRIC

TANRIC uses NG-CHMs for its heatmap visualizations. To access the heat maps:

• Click the data use agreement.
• Click the Visualization button.
• Select a cancer type.
• Select the number of clusters (K).
• Click on one of the heatmap thumbnails.

REFLECT

REFLECT is a bioinformatics tool that aims to accelerate drug discovery and clinical translation that will result in real patient benefit by identifying co-actionable, co-occurring oncogenic alterations that are recurrent within patient cohorts.

To access the hosted NG-CHMs:

• Select a Data Type.
• Select a Patient Stratification.
• Click the Go button.

Standardized Data

Test: Please refer to this page How to capture high quality images for publication

F1000Research

F1000Research is an open, peer-reviewed publishing platform for papers in all research areas. They accept NG-CHMs as interactive content within papers.

Our own NG-CHM paper is an example. Scroll down to the box labelled NG-CHM and click the Interactive Content button.

We encourage you to include interactive NG-CHMs in your papers and publish them in F1000Research.