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bioRxiv · 10.1101/359539

BindSpace: decoding transcription factor binding signals by large-scale joint embedding

Yuan, H.·Kshirsagar, M.·Zamparo, L.·Lu, Y.·Leslie, C. S.
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Abstract

Decoding transcription factor (TF) binding signals in genomic DNA is a fundamental problem. Here we present a prediction model called BindSpace that learns to embed DNA sequences and TF class/family labels into the same space. By training on binding data for hundreds of TFs and embedding over 1M DNA sequences, BindSpace achieves state-of-the-art multiclass binding prediction performance, in vitro and in vivo, and can distinguish signals of closely related TFs.

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Yuan, H., Kshirsagar, M., Zamparo, L., Lu, Y., Leslie, C. S.. 2018-06-29. BindSpace: decoding transcription factor binding signals by large-scale joint embedding. https://doi.org/10.1101/359539

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