I want to run the experiments "Sample Application to Genotype-Tissue Expression (GTEx) Project Gene Expression Data of Postmortem Tissues" mentioned in "Enter the Matrix: Factorization Uncovers Knowledge from Omics" by Stein-O'Brien et.al link

The paper metioned

dataset from postmortem samples in the GTEx project [42] (Figure 3). Specifically, we select a subset of GTEx data containing 12 brain tissues in the GTEx data for seven individuals for which we had previously performed only NMF analysis [41] (codes are provided in the supplemental information online).

I check with https://gtexportal.org/home/datasets and assumed that the paper used the GTEx Analysis V6.

But which files do I need to download? I am computer scientist I am unsure which ones contain the brain tissues

Further I found

Brain_Anterior_cingulate_cortex_BA24_Analysis_cis-eQTLs.txt.gz  1.5G
Brain_Caudate_basal_ganglia_Analysis_cis-eQTLs.txt.gz   1.9G
Brain_Cerebellar_Hemisphere_Analysis_cis-eQTLs.txt.gz   1.7G
Brain_Cerebellum_Analysis_cis-eQTLs.txt.gz  1.9G
Brain_Cortex_Analysis_cis-eQTLs.txt.gz  1.9G

But I am unsure which one was used in the paper



Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.