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

ABSTRACT: We developed Lisa (http://lisa.cistrome.org/) 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.

SUBMITTER: Qin Q

PROVIDER: S-EPMC7007693 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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

Qin Qian Q Fan Jingyu J Zheng Rongbin R Wan Changxin C Mei Shenglin S Wu Qiu Q Sun Hanfei H Brown Myles M Zhang Jing J Meyer Clifford A CA Liu X Shirley XS

Genome biology 20200207 1

We developed Lisa (http://lisa.cistrome.org/) 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 fr ...[more]

PMID: 32033573

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