Cross-platform DNA motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors.

ABSTRACT: A DNA sequence pattern, or "motif", is an essential representation of DNA-binding specificity of a transcription factor (TF). Any particular motif model has potential flaws due to shortcomings of the underlying experimental data and computational motif discovery algorithm. As a part of the Codebook/GRECO-BIT initiative, here we evaluated at large scale the cross-platform recognition performance of positional weight matrices (PWMs), which remain popular motif models in many practical applications. We applied ten different DNA motif discovery tools to generate PWMs from the "Codebook" data comprised of 4,237 experiments from five different platforms profiling the DNA-binding specificity of 394 human proteins, focusing on understudied transcription factors of different structural families. Fo

SUBMITTER: Vorontsov IE 

PROVIDER: S-EPMC11601219 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature