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 labeled with target. Since our server is not powerful enough to run a large number of jobs, jobs submitted by scripts will be canceled. For users who have jobs with more than 20 gene sets, please use the latest local command line version of Lisa at GitHub. If you encounter any issue, please refer to our video tutorial or contact lisa@jimmy.harvard.edu by mailing your submitted job id(s). Tips: sometimes jobs stuck at 0% progress, there are two reasons: 1. input gene sets are not valid because they are not from standard RefSeq, Entrez or Ensembl, or gene symbols, please check your input ids or symbols; 2. our web server stops working due to large number of submitted jobs, please email us to restart web server(thanks:)), or use our local command line versions Lisa1 or Lisa2. 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.
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