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 compendia of public histone mark ChIP-seq and chromatin accessibility profiles to construct a chromatin model related to the regulation of these genes. Then 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.
Footnotes
List of abbreviations
- TF
- transcription factor
- CR
- chromatin regulator
- TR
- transcriptional regulator
- RP
- regulatory potential
- ISD
- in silico deletion
- ROC
- receiver operator characteristic
- AUC
- area under curve
- ChIP-seq
- chromatin immunoprecipitation followed by DNA sequencing
- DNase-seq
- DNase I digestion followed by DNA sequencing
- H3K27ac
- histone H3 lysine 27 acetylation
- AR
- Androgen Receptor
- ER
- Estrogen Receptor
- GR
- Glucocorticoid Receptor
Copyright
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Posted November 18, 2019.
Inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data
