Xavier Bofill-De Ros1, Brian Luke2, Robert Guthridge2,3, Uma Mudunuri2,3, Michael Loss2,3, Shuo Gu1. 1. RNA Mediated Gene Regulation Section, RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute. 2. Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research. 3. Leidos Biomedical Research Inc.
Abstract
MicroRNAs (miRNAs) are master regulators of gene expression in cancers. Their sequence variants or isoforms (isomiRs) are highly abundant and possess unique functions. Given their short sequence length and high heterogeneity, mapping isomiRs can be challenging; without adequate depth and data aggregation, low frequency events are often disregarded. To address these challenges, we present the Tumor IsomiR Encyclopedia (TIE): a dynamic database of isomiRs from over 10,000 adult and pediatric tumor samples in The Cancer Genome Atlas (TCGA) and The Therapeutically Applicable Research to Generate Effective Treatments (TARGET) projects. A key novelty of TIE is its ability to annotate heterogeneous isomiR sequences and aggregate the variants obtained across all datasets. Results can be browsed online or downloaded as spreadsheets. Here we show analysis of isomiRs of miR-21 and miR-30a to demonstrate the utility of TIE. AVAILABILITY AND IMPLEMENTATION: TIE search engine and data is freely available to use at https://isomir.ccr.cancer.gov/. Published by Oxford University Press 2021.
MicroRNAs (miRNAs) are master regulators of gene expression in cancers. Their sequence variants or isoforms (isomiRs) are highly abundant and possess unique functions. Given their short sequence length and high heterogeneity, mapping isomiRs can be challenging; without adequate depth and data aggregation, low frequency events are often disregarded. To address these challenges, we present the Tumor IsomiR Encyclopedia (TIE): a dynamic database of isomiRs from over 10,000 adult and pediatric tumor samples in The Cancer Genome Atlas (TCGA) and The Therapeutically Applicable Research to Generate Effective Treatments (TARGET) projects. A key novelty of TIE is its ability to annotate heterogeneous isomiR sequences and aggregate the variants obtained across all datasets. Results can be browsed online or downloaded as spreadsheets. Here we show analysis of isomiRs of miR-21 and miR-30a to demonstrate the utility of TIE. AVAILABILITY AND IMPLEMENTATION: TIE search engine and data is freely available to use at https://isomir.ccr.cancer.gov/. Published by Oxford University Press 2021.
Authors: Ryan D Morin; Michael D O'Connor; Malachi Griffith; Florian Kuchenbauer; Allen Delaney; Anna-Liisa Prabhu; Yongjun Zhao; Helen McDonald; Thomas Zeng; Martin Hirst; Connie J Eaves; Marco A Marra Journal: Genome Res Date: 2008-02-19 Impact factor: 9.043
Authors: Antonina Parafioriti; Ingrid Cifola; Clarissa Gissi; Eva Pinatel; Laura Vilardo; Elisabetta Armiraglio; Andrea Di Bernardo; Primo Andrea Daolio; Armando Felsani; Igea D'Agnano; Anna Concetta Berardi Journal: Cell Death Discov Date: 2020-06-10