Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data

Genome Biol. 2020 Feb 7;21(1):32. doi: 10.1186/s13059-020-1934-6.


We developed Lisa ( to predict the transcriptional regulators (TRs) of differentially expressed or co-expressed gene sets. Based on the input gene sets, Lisa first uses histone mark ChIP-seq and chromatin accessibility profiles to construct a chromatin model related to the regulation of these genes. Using TR ChIP-seq peaks or imputed TR binding sites, Lisa probes the chromatin models using in silico deletion to find the most relevant TRs. Applied to gene sets derived from targeted TF perturbation experiments, Lisa boosted the performance of imputed TR cistromes and outperformed alternative methods in identifying the perturbed TRs.

Keywords: Chromatin accessibility; DNase-seq; Differential gene expression; Gene regulation; Gene set analysis; H3K27ac ChIP-seq; Transcription factors.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromatin / chemistry
  • Chromatin / genetics
  • Chromatin / metabolism
  • Chromatin Immunoprecipitation Sequencing / methods*
  • Databases, Genetic
  • Histone Code
  • Humans
  • Software*
  • Transcription Factors / metabolism*


  • Chromatin
  • Transcription Factors