Journal
GENOME BIOLOGY
Volume 21, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/s13059-020-1934-6
Keywords
Transcription factors; Gene regulation; Chromatin accessibility; DNase-seq; Differential gene expression; Gene set analysis
Funding
- NIH [U24 HG009446, U24 CA237617]
- National Natural Science Foundation of China [31801110]
- Shanghai Sailing Program [18YF1402500]
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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.
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