SNPeBoT: a tool for predicting transcription factor allele specific binding

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  • dc.contributor.author Gohl, Patrick
  • dc.contributor.author Oliva Miguel, Baldomero
  • dc.date.accessioned 2025-05-05T06:24:06Z
  • dc.date.available 2025-05-05T06:24:06Z
  • dc.date.issued 2025
  • dc.description.abstract Background: Mutations in non-coding regulatory regions of DNA may lead to disease through the disruption of transcription factor binding. However, our understanding of binding patterns of transcription factors and the effects that changes to their binding sites have on their action remains limited. To address this issue we trained a Deep learning model to predict the effects of Single Nucleotide Polymorphisms (SNP) on transcription factor binding. Allele specific binding (ASB) data from Chromatin Immunoprecipitation sequencing (ChIP-seq) experiments were paired with high sequence-identity DNA binding Domains assessed in Protein Binding Microarray (PBM) experiments. For each transcription factor a paired DNA binding Domain was selected from which we derived E-score profiles for reference and alternate DNA sequences of ASB events. A Convolutional Neural Network (CNN) was trained to predict whether these profiles were indicative of ASB gain/loss or no change in binding. 18211 E-score profiles from 113 transcription factors were split into train, validation and test data. We compared the performance of the trained model with other available platforms for predicting the effect of SNP on transcription factor binding. Our model demonstrated increased accuracy and ASB recall in comparison to the best scoring benchmark tools. Conclusion: In this paper we present our model SNPeBoT (Single Nucleotide Polymorphism effect on Binding of Transcription Factors) in its standalone and web server form. The increased recovery and prediction accuracy of allele specific binding events could prove useful in discovering non-coding mutations relevant to disease.
  • dc.description.sponsorship The work was supported by grants PID2020-113203RB-I00, PID2023-150068OB-I00 and “Unidad de Excelencia María de Maeztu” (ref: CEX2018-000792-M), funded by the MCIN and the AEI https://doi.org/10.13039/501100011033, MCIUN/AEI/10.13039/501100011033/FEDER, UE as well as an FPU scholarship (ref: FPU22/02303) and an SGR from the Generalitat de Catalunya (ref: 4413015318- J.SELENT/SGR-22).
  • dc.format.mimetype application/pdf
  • dc.identifier.citation Gohl P, Oliva B. SNPeBoT: a tool for predicting transcription factor allele specific binding. BMC Bioinformatics. 2025 Mar 10;26(1):81. DOI: 10.1186/s12859-025-06094-4
  • dc.identifier.doi http://dx.doi.org/10.1186/s12859-025-06094-4
  • dc.identifier.issn 1471-2105
  • dc.identifier.uri http://hdl.handle.net/10230/70281
  • dc.language.iso eng
  • dc.publisher BioMed Central
  • dc.relation.ispartof BMC Bioinformatics. 2025 Mar 10;26(1):81
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/PID2020-113203RB-I00
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/3PE/PID2023-150068OB-I00
  • dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/CEX2018-000792-M
  • dc.rights © The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.
  • dc.rights.accessRights info:eu-repo/semantics/openAccess
  • dc.rights.uri http://creativecommons.org/licenses/by-nc-nd/4.0/
  • dc.subject.keyword Gene regulation
  • dc.subject.keyword Neural network
  • dc.subject.keyword Transcription factor
  • dc.title SNPeBoT: a tool for predicting transcription factor allele specific binding
  • dc.type info:eu-repo/semantics/article
  • dc.type.version info:eu-repo/semantics/publishedVersion

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