I am interested in analyzing the correlation between the expression of a set of genes and transposable elements (TEs) in cancer. However, despite there are multiple online databases for gene expression in cancer, including TCGA, they do not include repetitive elements. Despite I've found some papers analyzing transposable elements and quantifying their expression in different cancer using TCGA data, supplemental tables only provide the fold change end p-values for differentially expressed TEs. Also, to identify and quantify TEs, the raw sequencing data, which have controlled access, would be necessary. Therefore, I was wondering if there is some database or published resource where I could find information regarding TE expression per sample in TCGA database. Does someone know something like that? Alternatively, if someone have analyzed this type of data and have some worksheet with pre-processed data that could be shared, I would be deeply grateful.
Hi Glauco,
Are you aware of the Xena browser (https://xenabrowser.net/)? There are at least gene expression, mutation and methylation data per patient for the TCGA cohorts. Unfortunately I am not sure about the TE data, since I am not working with that but I think that Xena would be your best bet.
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