saarantras1/mpac-mpra

MPAC and Malinois MPRA data

MPRA-measured regulatory activity of 798,064 unique oligos in K562, HepG2 and SK-N-SH. This is the dataset behind both Malinois and MPAC; MPAC is the same data re-split into chromosome-pair folds.

The papers are the source of truth for how this data was generated and used: Gosai et al., Nature 2024 and Butts et al., bioRxiv 2025.

Provenance

Table_S2__MPRA_dataset.tsv is Supplementary Table 2 of Gosai et al., included verbatim. It is byte-identical to DATA-Table_S2__MPRA_dataset.txt in Zenodo 10698014 and to the Nature supplementary file 41586_2024_8070_MOESM4_ESM.txt (md5 a1b36bb5e270b6414e74f2a83ea47e5d). The raw per-library MPRA output and the notebooks that aggregate it are in the same Zenodo record.

Per Gosai et al. Methods, the training loop additionally discarded "oligos with a plasmid count of fewer than 20 or no RNA count in any cell type"; this table is the aggregation without the plasmid-count filter, which the paper deposits as the training data and uses for its analyses. Performance metrics in both papers omit oligos with a log2FC standard error above 1 in any cell type.

License

CC-BY-NC-4.0, matching the Zenodo deposit.

Citation

@article{gosai2024coda,
  title   = {Machine-guided design of cell-type-targeting cis-regulatory elements},
  author  = {Gosai, Sager J. and Castro, Rodrigo I. and Fuentes, Natalia and
             Butts, John C. and Mouri, Kousuke and Alasoadura, Michael and
             Kales, Susan and Nguyen, Thanh Thanh L. and Noche, Ramil R. and
             Rao, Arya S. and Joy, Mary T. and Sabeti, Pardis C. and
             Reilly, Steven K. and Tewhey, Ryan},
  journal = {Nature},
  year    = {2024},
  doi     = {10.1038/s41586-024-08070-z}
}

@article{butts2025mpac,
  title   = {Identifying non-coding variant effects at scale via machine learning
             models of cis-regulatory reporter assays},
  author  = {Butts, John C. and Rong, Stephen and Gosai, Sager J. and
             Castro, Rodrigo I. and Noon, Mackenzie and Adeniran, Kehinde and
             Ghosh, Rohit and Sabeti, Pardis C. and Tewhey, Ryan and Reilly, Steven K.},
  journal = {bioRxiv},
  year    = {2025},
  doi     = {10.1101/2025.04.16.648420}
}

@article{siraj2024mpra,
  title   = {Functional dissection of complex and molecular trait variants at
             single nucleotide resolution},
  author  = {Siraj, Layla and Castro, Rodrigo I. and Dewey, Hannah and others},
  journal = {bioRxiv},
  year    = {2024},
  doi     = {10.1101/2024.05.05.592437}
}