The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes
Abstract Background The precise prediction of transcription factor binding sites (TFBSs) is pivotal for unraveling the gene regulatory networks underlying biological processes. While numerous tools have emerged for in silico TFBS prediction in recent years, the evolving landscape of computational bi...
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2024-12-01
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| author | Dinithi V. Wanniarachchi Sameera Viswakula Anushka M. Wickramasuriya |
| author_facet | Dinithi V. Wanniarachchi Sameera Viswakula Anushka M. Wickramasuriya |
| author_sort | Dinithi V. Wanniarachchi |
| collection | DOAJ |
| description | Abstract Background The precise prediction of transcription factor binding sites (TFBSs) is pivotal for unraveling the gene regulatory networks underlying biological processes. While numerous tools have emerged for in silico TFBS prediction in recent years, the evolving landscape of computational biology necessitates thorough assessments of tool performance to ensure accuracy and reliability. Only a limited number of studies have been conducted to evaluate the performance of TFBS prediction tools comprehensively. Thus, the present study focused on assessing twelve widely used TFBS prediction tools and four de novo motif discovery tools using a benchmark dataset comprising real, generic, Markov, and negative sequences. TFBSs of Arabidopsis thaliana and Homo sapiens genomes downloaded from the JASPAR database were implanted in these sequences and the performance of tools was evaluated using several statistical parameters at different overlap percentages between the lengths of known and predicted binding sites. Results Overall, the Multiple Cluster Alignment and Search Tool (MCAST) emerged as the best TFBS prediction tool, followed by Find Individual Motif Occurrences (FIMO) and MOtif Occurrence Detection Suite (MOODS). In addition, MotEvo and Dinucleotide Weight Tensor Toolbox (DWT-toolbox) demonstrated the highest sensitivity in identifying TFBSs at 90% and 80% overlap. Further, MCAST and DWT-toolbox managed to demonstrate the highest sensitivity across all three data types real, generic, and Markov. Among the de novo motif discovery tools, the Multiple Em for Motif Elicitation (MEME) emerged as the best performer. An analysis of the promoter regions of genes involved in the anthocyanin biosynthesis pathway in plants and the pentose phosphate pathway in humans, using the three best-performing tools, revealed considerable variation among the top 20 motifs identified by these tools. Conclusion The findings of this study lay a robust groundwork for selecting optimal TFBS prediction tools for future research. Given the variability observed in tool performance, employing multiple tools for identifying TFBSs in a set of sequences is highly recommended. In addition, further studies are recommended to develop an integrated toolbox that incorporates TFBS prediction or motif discovery tools, aiming to streamline result precision and accuracy. |
| format | Article |
| id | doaj-art-dcdfc01c8a8b46d2953eb6a296990967 |
| institution | Kabale University |
| issn | 1471-2105 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj-art-dcdfc01c8a8b46d2953eb6a2969909672024-12-08T12:47:36ZengBMCBMC Bioinformatics1471-21052024-12-0125112510.1186/s12859-024-05995-0The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomesDinithi V. Wanniarachchi0Sameera Viswakula1Anushka M. Wickramasuriya2Department of Plant Sciences, Faculty of Science, University of ColomboDepartment of Statistics, Faculty of Science, University of ColomboDepartment of Plant Sciences, Faculty of Science, University of ColomboAbstract Background The precise prediction of transcription factor binding sites (TFBSs) is pivotal for unraveling the gene regulatory networks underlying biological processes. While numerous tools have emerged for in silico TFBS prediction in recent years, the evolving landscape of computational biology necessitates thorough assessments of tool performance to ensure accuracy and reliability. Only a limited number of studies have been conducted to evaluate the performance of TFBS prediction tools comprehensively. Thus, the present study focused on assessing twelve widely used TFBS prediction tools and four de novo motif discovery tools using a benchmark dataset comprising real, generic, Markov, and negative sequences. TFBSs of Arabidopsis thaliana and Homo sapiens genomes downloaded from the JASPAR database were implanted in these sequences and the performance of tools was evaluated using several statistical parameters at different overlap percentages between the lengths of known and predicted binding sites. Results Overall, the Multiple Cluster Alignment and Search Tool (MCAST) emerged as the best TFBS prediction tool, followed by Find Individual Motif Occurrences (FIMO) and MOtif Occurrence Detection Suite (MOODS). In addition, MotEvo and Dinucleotide Weight Tensor Toolbox (DWT-toolbox) demonstrated the highest sensitivity in identifying TFBSs at 90% and 80% overlap. Further, MCAST and DWT-toolbox managed to demonstrate the highest sensitivity across all three data types real, generic, and Markov. Among the de novo motif discovery tools, the Multiple Em for Motif Elicitation (MEME) emerged as the best performer. An analysis of the promoter regions of genes involved in the anthocyanin biosynthesis pathway in plants and the pentose phosphate pathway in humans, using the three best-performing tools, revealed considerable variation among the top 20 motifs identified by these tools. Conclusion The findings of this study lay a robust groundwork for selecting optimal TFBS prediction tools for future research. Given the variability observed in tool performance, employing multiple tools for identifying TFBSs in a set of sequences is highly recommended. In addition, further studies are recommended to develop an integrated toolbox that incorporates TFBS prediction or motif discovery tools, aiming to streamline result precision and accuracy.https://doi.org/10.1186/s12859-024-05995-0Transcription factor binding sitesBioinformatics toolsPerformance evaluation |
| spellingShingle | Dinithi V. Wanniarachchi Sameera Viswakula Anushka M. Wickramasuriya The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes BMC Bioinformatics Transcription factor binding sites Bioinformatics tools Performance evaluation |
| title | The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes |
| title_full | The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes |
| title_fullStr | The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes |
| title_full_unstemmed | The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes |
| title_short | The evaluation of transcription factor binding site prediction tools in human and Arabidopsis genomes |
| title_sort | evaluation of transcription factor binding site prediction tools in human and arabidopsis genomes |
| topic | Transcription factor binding sites Bioinformatics tools Performance evaluation |
| url | https://doi.org/10.1186/s12859-024-05995-0 |
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