Description

Massively Parallel Reporter Assays (MPRAs) are high-throughput experimental methods that measure transcriptional output of thousands of short DNA sequences using sequencing. If in addition, a mutated sequence is tested, the impact of a genetic variant can be quantified.

This track collection brings together results from two MPRA databases, one for the complete sequence fragments, one for the impact of variants in selected fragments:

• MPRA Base — 41,275 experimentally tested cis-regulatory elements from 51 MPRA, STARR-seq, and related reporter assay experiments, curated in the MPRA Base database (Zhao et al., 2023).
• MPRAVarDB — 242,818 variants from 18 MPRA studies, tested for effects on transcriptional regulatory activity across over 30 cell lines and 30 human diseases and traits (Wang et al., 2024).

Data Access

See the individual subtrack documentation pages linked above for detailed information on how to download and intersect the annotations.

Credits

Thanks to Tao Wang and colleagues at the University of Florida for MPRAVarDB, and to Varda Singhal and the Ahituv Lab at the University of California San Francisco for MPRA Base.

References

Wang T, Matreyek KA, Yang X. MPRAVarDB: an online database and web server for exploring regulatory effects of genetic variants using MPRA data. Bioinformatics. 2024 Apr 15;40(4):btae201. PMID: 38617248; PMC: PMC11014600

Zhao J, Baltoumas FA, Konnaris MA, Mouratidis I, Liu Z, Sims J, Agarwal V, Pavlopoulos GA, Georgakopoulos-Soares I, Ahituv N. MPRAbase: A Massively Parallel Reporter Assay Database. bioRxiv. 2023 Nov 22;. PMID: 38045264; PMC: PMC10690217