GTEx compendium expression plot legend

[Elo Madissoon]

Hi!

I'm using Investigate Gene Sets - Compendia Expression Profiles - GTEx compendium to display the expression of genes of interest. I can't find a legend for the heatmap expression values or for the lineage color codes. Could you point me in the right direction?

Thank you in advance,
Elo

[Anthony Castanza]

Hi Elo,

 

Unfortunately, the website doesn’t generate a legend for the heatmap. Ultimately, it uses the same code as the standard heatmaps in GSEA results with a red-high expression, blue-low expression color scale.

The gene expression data underlying this dataset is from https://gtexportal.org/home/datasets, specifically:

https://storage.googleapis.com/gtex_analysis_v8/rna_seq_data/GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_median_tpm.gct.gz where this data has been converted to Human Gene Symbols using the MSigDB CHIP files.

 

We’re working on integrating a new renderer for these heat maps, but it’s still in the early stages.

If you absolutely need a legend for heatmap, generating your own using the underlying data and your genes of interest might be the best way to go.

 

Sorry I couldn’t be of more help here, I’ll make a note that this is a critical feature to include in the next version of this tool.

-Anthony

 

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

http://gsea-msigdb.org/

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