Tumor IsomiR Encyclopedia - Gu-Lab-RBL-NCI/TIE-database GitHub Wiki
MicroRNAs (miRNAs) function as master regulators of gene expression in many physiological and pathological conditions including cancer. Sequence variants or isoforms (isomiRs) can range between 40 to 60% of total miRNA counts, despite overwhelming abundance, their function continues to be debated. Recent studies demonstrate that certain isomiRs can regulate unique sets of target mRNAs by altering their seed sequence or stabilizing 3’ pairing, while others are decay intermediates indicating an active miRNA turnover. Given their short sequence and high heterogeneity, mapping isomiRs can be complex. Also, without adequate depth and data aggregation, low frequency events can be easily 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 the ability to annotate heterogeneous isomiR sequences and aggregate the variants obtained across all samples and datasets. The database provides annotation of templated and non-templated nucleotides as well as other advanced analysis. All data can be downloaded as plain spreadsheets. TIE search engine and data are hosted at https://isomir.ccr.cancer.gov/.
Database sections:
- Tumor IsomiR Encyclopedia
- Run query
- Align files
- IsomiRs annotated
- 5’ isomiRs analysis
- Nucleotide composition by position
- Dendrogram and Distance Matrix Files
- Performance Summary
QuagmiR algorithm
Citation:
- QuagmiR: A Cloud-based Application for IsomiR Big Data Analytics. Bofill-De Ros X, Chen K, Chen S, Tesic N, Randjelovic D, Skundric N, Nesic S, Varjacic V, Williams EH, Malhotra R, Jiang M, Gu S. Bioinformatics. 2018 Oct 8. doi: 10.1093/bioinformatics/bty843.
- Tumor IsomiR Encyclopedia (TIE): a pan-cancer database of miRNA isoforms. Bofill-De Ros X, Luke B, Guthridge R, Mudunuri U, Loss M, Gu S. [submitted]