TFEBexplorer: An integrated tool to study genes regulated by the stress-responsive Transcription Factor EB

Abstract

TFEBexplorer is a comprehensive web-tool to study genes modulated by the transcription factor EB (TFEB), a master regulator of lysosomal biogenesis and autophagy, that integrates multiple datasets following genetic perturbation of TFEB with experimentally validated and bioinformatically-predicted binding sites across multiple species. Given one gene, or a set of genes of interest, in input (query), the results are displayed in different panels, each reporting results of experiments or bioinformatic analyses. TFEBdb is a unique resource for those interested in understanding the effect of TFEB on a set of genes of interest. The database offers an intuitive interface and results are displayed in an easy-to-interpret format offering information on the expression changes following inducible over-expression, knock-down and knock-out of TFEB across cell lines and species together with experimentally validated and bioinformatically predicted binding sites in the proximal promoter of the gene(s) of interest. The TFEBdb homepage can be found at http://tfeb.tigem.it. Abbreviations ChIP-seq: chromatin-immunoprecipitation followed by sequencing; CLEAR: Coordinated Lysosomal Expression and Regulation; DMEM: Dulbecco’s modified Eagle’s medium; FDR: False discovery rate; GEPs: gene expression profiles; PBS: phosphate-buffered saline; RMA: robust multiarray average TFEB: The transcription factor EB; TFEBdb: database; ToA: time of activation of the gene.

Keywords

• autophagy
• binding site
• gene expression
• lysosome
• tfeb