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Published April 27, 2023 | Version v3
Dataset Open

Multimodal learning of noncoding variant effects using genome sequence and chromatin structure

Authors/Creators

  • 1. Texas A&M University

Description

ncVarPred-1D3D: pretrained models of Sei (PMID: 35817977) + our 3D structure embedding models are shared. The models are trained and validated using DeepSEA (PMID: 26301843) selected 200 bp regions (we extended to 4K bp neighboring) to predict the epigenetic profile containing 21907 epigenetic events Sei processed.

The pretrained DeepSEA (PMID: 26301843) and reproduced DanQ (PMID: 27084946) can be found in SOTA.tar.gz.

Files

Files (34.0 GB)

Name Size Download all
md5:7b2adfbf9c9beed1cd72860cb35c0988
20.0 GB Download
md5:5693c612d9639bd69f0ea3a1135d6204
10.3 GB Download
md5:c4556f8571a3d3a467ebc333643dbdf2
3.6 GB Download

Additional details

References

  • Tan, Wuwei, and Yang Shen. "Multimodal learning of noncoding variant effects using genome sequence and chromatin structure." bioRxiv (2022): 2022-12.