spatzie: an R package for identifying significant transcription factor motif co-enrichment from enhancer–promoter interactions
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gkac036.pdf
Description
Published version
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546.41 KB
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Author(s)
Hammelman, Jennifer
Krismer, Konstantin
Gifford, David K
Date Issued
2022
Journal
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Citation
Hammelman, Jennifer, Krismer, Konstantin and Gifford, David K. 2022. "spatzie: an R package for identifying significant transcription factor motif co-enrichment from enhancer–promoter interactions." Nucleic Acids Research, 50 (9).
Version
Final published version
Abstract
Abstract
Genomic interactions provide important context to our understanding of the state of the genome. One question is whether specific transcription factor interactions give rise to genome organization. We introduce spatzie, an R package and a website that implements statistical tests for significant transcription factor motif cooperativity between enhancer–promoter interactions. We conducted controlled experiments under realistic simulated data from ChIP-seq to confirm spatzie is capable of discovering co-enriched motif interactions even in noisy conditions. We then use spatzie to investigate cell type specific transcription factor cooperativity within recent human ChIA-PET enhancer–promoter interaction data. The method is available online at https://spatzie.mit.edu.
Genomic interactions provide important context to our understanding of the state of the genome. One question is whether specific transcription factor interactions give rise to genome organization. We introduce spatzie, an R package and a website that implements statistical tests for significant transcription factor motif cooperativity between enhancer–promoter interactions. We conducted controlled experiments under realistic simulated data from ChIP-seq to confirm spatzie is capable of discovering co-enriched motif interactions even in noisy conditions. We then use spatzie to investigate cell type specific transcription factor cooperativity within recent human ChIA-PET enhancer–promoter interaction data. The method is available online at https://spatzie.mit.edu.
MIT Department
Massachusetts Institute of Technology. Computational and Systems Biology Program
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
Massachusetts Institute of Technology. Department of Biological Engineering
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Creative Commons Attribution 4.0 International license
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DOI of Published Version
https://doi.org/10.1093/NAR/GKAC036
