ArticleCommunications biology2025
Cross-platform motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors.
Article in Communications biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Article
- GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors.Nature methods · 2026Article
- Identification of methylation-sensitive human transcription factors using meSMiLE-seq.Nature communications · 2026Article
- Extensive binding of poorly characterized human transcription factors to genomic dark matter.Nature communications · 2026Article
- Inferring binding specificities of human transcription factors with the wisdom of crowds.bioRxiv : the preprint server for biology · 2025Article
- Perspectives on Codebook: sequence specificity of uncharacterized human transcription factors.bioRxiv : the preprint server for biology · 2024Article
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35 authors.
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Abstract
A sequence motif representing the DNA-binding specificity of a transcription factor (TF) is commonly modelled with a positional weight matrix (PWM). Focusing on understudied human TFs, we processed results of 4,237 experiments for 394 TFs, assayed using five different experimental platforms. By human curation, we approved a subset of experiments that yielded consistent motifs across platforms and replicates, and evaluated quantitatively the cross-platform performance of PWMs obtained with ten motif discovery tools. Notably, nucleotide composition and information content are not correlated with motif performance and do not help in detecting underperformers, while motifs with low information content, in many cases, describe well the binding specificity assessed across different experimental platforms. By combining multiple PMWs into a random forest, we demonstrate the potential of accounting for multiple modes of TF binding. Finally, we present the Codebook Motif Explorer ( https://mex.autosome.org ), cataloguing motifs, benchmarking results, and the underlying experimental data.
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