Lisa

Overview

epigenetic Landscape In Silico deletion Analysis

The motivation of Lisa is to use public along with in-house chromatin profile data from a comprehensive database of human and mouse DNase-seq, and H3K27ac ChIP-seq profiles, to determine the transcription factors and chromatin regulators that are directly responsible for the perturbation of a differentially expressed gene set. To run Lisa, the only thing you need is the differential gene list from whatever biological process you are interested in. The gene set can be constituted of only official gene symbols, only RefSeq ids, or only Ensembl ids, or only Entrez ids, or a mixture of these identifiers. Then you will be able to leverage the power of the most comprehensive DNase and ChIP-seq database (CistromeDB) to discover the key transcription factors and chromatin regulators. One tip for viewing the TR ranking table is to click on those p-values, a Cistrome DB page will come along, also the TR-target gene pair list is provided in the downloaded results with file name labelled with target. For users who have plenty of gene sets (more than 10 gene lists), please use the latest local command line version of Lisa at GitHub, since our server is not powerful enough to run large amount of jobs, large amount of programmed submitted jobs will be killed and affect other users's normal usage. If you encounter any issue, please refer to our video tutorial or contact lisa@jimmy.harvard.edu by mailing your submitted job id(s). If you like the tool, please cite Qin Q, Fan J, Zheng R, Wan C, Mei S, Wu Q, et al. Inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data. Genome Biology;(2020)21:32.

Documentation
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