SEMpl

SEMpl (SNP Effect Matrix Pipeline) is a computational tool that predicts the impact of noncoding single-nucleotide polymorphisms (SNPs) on transcription factor binding. Most disease-associated SNPs are found in noncoding regions, making it challenging to prioritize them for experimental validation. SEMpl addresses this issue by estimating changes in transcription factor-binding affinity caused by SNPs within functional transcription factor-binding sites (TFBSs) across the genome.

The pipeline utilizes chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) data to observe differences in signal intensity for SNPs within TFBSs. By cataloging the effects of all possible mutations within the TFBS motif, SEMpl can predict the consequences of SNPs on transcription factor binding. This information can identify potential disease-causing regulatory loci, facilitating the prioritization of noncoding SNPs for further experimental validation.

Topic

Transcription factors and regulatory sites;DNA polymorphism;ChIP-seq

Detail

  • Operation: SNP annotation;Transcription factor binding site prediction;Nucleic acids-binding site prediction

  • Software interface: Command-line user interface

  • Language: C++

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: National Institutes of Health, University of Michigan Undergraduate Research Opportunity Program.

  • Input: -

  • Output: -

  • Contact: Alan P Boyle apboyle@umich.edu

  • Collection: -

  • Maturity: -

Publications

  • Predicting the effects of SNPs on transcription factor binding affinity.
  • Nishizaki SS, et al. Predicting the effects of SNPs on transcription factor binding affinity. Predicting the effects of SNPs on transcription factor binding affinity. 2020; 36:364-372. doi: 10.1093/bioinformatics/btz612
  • https://doi.org/10.1093/BIOINFORMATICS/BTZ612
  • PMID: 31373606
  • PMC: PMC7999143

Download and documentation

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