tRNA fragment profiles of TCGA by MINTmap | Computational Medicine Center at Thomas Jefferson University

In this page we provide the tRNA fragment (tRF) profiles of The Cancer Genome Atlas (TCGA). The profiles have been produced using MINTmap¹, our tRNA fragment (tRF) mining tool. You can explore them interactively using MINTbase², our tRF database.

The profiles present in this page have been used by our 2019 paper³ and released as compressed files per dataset, per cancer, and for the entire TCGA. Please continue below to find out how to download each format.

Download compressed MINTmap tRNA fragment profiles per cancer

Click on the buttons below to download the compressed TCGA tRNA fragment profiles for a specific cancer (e.g. BRCA) or for all cancers (All projects).

Download compressed MINTmap tRNA fragment profiles per TCGA dataset

We also have made available a compressed downloadable file per TCGA dataset. You can browse them by pressing the button below.

Browse

Use MINTbase to view the profiles

Use MINTbase to explore the expression of each tRF per cancer, the tRNA origins and tRF expression patterns per cancer, etc. MINTbase contains a variety of other datasets and projects, besides TCGA, and offers download options per tRF and per search. You can visit MINTbase by clicking this link or the image below.

MINTbase, the database of tRNA fragment profiles of TCGA and other projects

References

Loher, P, Telonis, AG, Rigoutsos, I. MINTmap: fast and exhaustive profiling of nuclear and mitochondrial tRNA fragments from short RNA-seq data. Sci Rep. 2017;7 :41184. doi: 10.1038/srep41184. PubMed PMID:28220888 PubMed Central PMC5318995.
Pliatsika, V, Loher, P, Magee, R, Telonis, AG, Londin, E, Shigematsu, M, Kirino, Y, Rigoutsos, I. MINTbase v2.0: a comprehensive database for tRNA-derived fragments that includes nuclear and mitochondrial fragments from all The Cancer Genome Atlas projects. Nucleic Acids Res. 2018;46 (D1):D152-D159. doi: 10.1093/nar/gkx1075. PubMed PMID:29186503 PubMed Central PMC5753276.
Telonis, AG, Loher, P, Magee, R, Pliatsika, V, Londin, E, Kirino, Y, Rigoutsos, I. tRNA Fragments Show Intertwining with mRNAs of Specific Repeat Content and Have Links to Disparities. Cancer Res. 2019 Apr 17. doi: 10.1158/0008-5472.CAN-19-0789. PubMed PMID:30996049.