ArticleNucleic acids research2022
spatzie: an R package for identifying significant transcription factor motif co-enrichment from enhancer-promoter interactions.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- GraphLooper: predicting chromatin loops based on hierarchical multi-view graph pooling method.Briefings in bioinformatics · 2026Article
- Guidelines on the performance evaluation of motif recognition methods in bioinformatics.Frontiers in genetics · 2023Article
- DLoopCaller: A deep learning approach for predicting genome-wide chromatin loops by integrating accessible chromatin landscapes.PLoS computational biology · 2022Article
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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.
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