Document Type

Article

Publication Date

1-1-2018

Comments

This is an article accepted for publication in Nucleic Acids Research following peer review. The version of record Pliatsika, V., Loher, P., Magee, R., Telonis, A. G., Londin, E., Shigematsu, M., Kirino, Y., & Rigoutsos, I. (2018). 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 Research, 46(D1), D152-D159. is available online at: https://doi.org/10.1093/nar/gkx1075


Abstract

MINTbase is a repository that comprises nuclear and mitochondrial tRNA-derived fragments ('tRFs') found in multiple human tissues. The original version of MINTbase comprised tRFs obtained from 768 transcriptomic datasets. We used our deterministic and exhaustive tRF mining pipeline to process all of The Cancer Genome Atlas datasets (TCGA). We identified 23 413 tRFs with abundance of ≥ 1.0 reads-per-million (RPM). To facilitate further studies of tRFs by the community, we just released version 2.0 of MINTbase that contains information about 26 531 distinct human tRFs from 11 719 human datasets as of October 2017. Key new elements include: the ability to filter tRFs on-the-fly by minimum abundance thresholding; the ability to filter tRFs by tissue keywords; easy access to information about a tRF's maximum abundance and the datasets that contain it; the ability to generate relative abundance plots for tRFs across cancer types and convert them into embeddable figures; MODOMICS information about modifications of the parental tRNA, etc. Version 2.0 of MINTbase contains 15x more datasets and nearly 4x more distinct tRFs than the original version, yet continues to offer fast, interactive access to its contents. Version 2.0 is available freely at http://cm.jefferson.edu/MINTbase/.

Creative Commons License

Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 License

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