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Assessing NGS-based computational methods for predicting transcriptional regulators with query gene sets.

Zeyu LuXue XiaoQiang ZhengXinlei WangLin Xu
Published in: bioRxiv : the preprint server for biology (2024)
An introduction to available computational methods for predicting functional TRs from a query gene set.A detailed walk-through along with practical concerns and limitations.A systematic benchmark of NGS-based methods in terms of accuracy, sensitivity, coverage, and usability, using 570 TR perturbation-derived gene sets.NGS-based methods outperform motif-based methods. Among NGS methods, those utilizing larger databases and adopting region-centric approaches demonstrate favorable performance. BART, ChIP-Atlas, and Lisa are recommended as these methods have overall better performance in evaluated scenarios.
Keyphrases
  • genome wide
  • gene expression
  • copy number
  • transcription factor
  • healthcare
  • health information
  • social media
  • artificial intelligence