YTLR: Extracting yeast transcription factor-gene associations from the literature using automated literature readers

Tzu Hsien Yang, Chung Yu Wang, Hsiu Chun Tsai, Ya Chiao Yang, Cheng Tse Liu

研究成果: Article同行評審

2 引文 斯高帕斯(Scopus)


Cells adapt to environmental stresses mainly via transcription reprogramming. Correct transcription control is mediated by the interactions between transcription factors (TF) and their target genes. These TF-gene associations can be probed by chromatin immunoprecipitation techniques and knockout experiments, revealing TF binding (TFB) and regulatory (TFR) evidence, respectively. Nevertheless, most evidence is still fragmentary in the literature and requires tremendous human resources to curate. We developed the first pipeline called YTLR (Yeast Transcription-regulation Literature Reader) to automate TF-gene relation extraction from the literature. YTLR first identifies articles with TFB and TFR information. Then TF-gene binding pairs are extracted from the TFB articles, and TF-gene regulatory associations are recognized from the TFR papers. On gathered test sets, YTLR achieves an AUC value of 98.8% in identifying articles with TFB evidence and AUC = 83.4% in extracting the detailed TF-gene binding pairs. And similarly, YTLR also obtains an AUC value of 98.2% in identifying TFR articles and AUC = 80.4% in extracting the detailed TF-gene regulatory associations. Furthermore, YTLR outperforms previous methods in both tasks. To facilitate researchers in extracting TF-gene transcriptional relations from large-scale queried articles, an automated and easy-to-use software tool based on the YTLR pipeline is constructed. In summary, YTLR aims to provide easier literature pre-screening for curators and help researchers gather yeast TF-gene transcriptional relation conclusions from articles in a high-throughput fashion. The YTLR pipeline software tool can be downloaded at

頁(從 - 到)4636-4644
期刊Computational and Structural Biotechnology Journal
出版狀態Published - 2022 1月

All Science Journal Classification (ASJC) codes

  • 生物技術
  • 生物物理學
  • 結構生物學
  • 生物化學
  • 遺傳學
  • 電腦科學應用


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