Homotypic motifs from 5 databases in the promoters of 21 plant species

What is this about:

This project encompasses multiple plant species, primarily employing tools like FIMO and PMET index to search for homotypic motifs in the promoters across various plant species. We selected five different sources of motifs: CIS-BP2, Franco-Zorrilla et al. 2014, Jaspar plants non redundant 2022, PlantTFDB and Plant Cistrome DB.

Our research delves into an extensive analysis of gene expression regulatory elements, aiming to unravel the mechanisms of plant gene expression regulation. For this purpose, we have pre-calculated a vast amount of data in order to identify promoter patterns that consistently appear across different species. These promoter patterns potentially play fundamental and crucial regulatory roles in each species.

How to use it:

All data are prepared for PMET-Shiny app: https://github.com/duocang/PMET-Shiny-App.

After downloading, all files are unzipped and put in the folder of data/indexing of PMET-Shiny.