najlaksouri/coexpression_motif_discovery

Discovering cis-regulatory motifs in proximal promoters of plants in RSAT::Plants

This repository documents recipes to discover cis-regulatory motifs within proximal promoters of plants in RSAT::Plants.

The reports and data in folder peach/ correspond to the benchmark experiment with peach expression-based gene modules. You can browse them at eead-csic-compbio.github.io/coexpression_motif_discovery/peach .

The recipes can be executed on the command-line with on a Docker container, as explained in the tutorial, or using the RSAT Web interfaces, as explained in the Web protocol.

Citation: N Ksouri(1), JA Castro-Mondragón (2,3), F Montardit-Tardà (1), J van Helden (2), B Contreras-Moreira (1,4,5), Y Gogorcena (1) (2021) Tuning promoter boundaries improves regulatory motif discovery in non-model plants: the peach example. Plant Physiology, https://doi.org/10.1093/plphys/kiaa091

Affiliations

1. Estación Experimental de Aula Dei-CSIC, Zaragoza, Spain
2. Aix-Marseille Univ, Theory and Approaches of Genome Complexity (TAGC), Marseille, France.
3. Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Norway.
4. Fundacion ARAID, Zaragoza, Spain
5. European Bioinformatics Institute EMBL-EBI, Hinxton, UK

Questions or comments, please contact: nksouri at eead.csic.es

Docker container

A docker container with Regulatory Sequence Analysis Tools (RSAT) image is available here. If you have not set a docker engine on your machine, please see the instructions provided by the docker community for a simplified installation procedure.

Once docker is set up, you can get and run the RSAT docker image by typing the following command lines in the terminal:

# Get the docker image
docker pull ksouri1/rsat_nksouri

# Run the docker container
docker run --rm -v ~/rsat_data:/packages/rsat/public_html/data/ -v ~/rsat_results:/home/rsat_user/rsat_results -it ksouri1/rsat_nksouri

“rsat_results” and “rsat_data” are two local directories in the host machine serving as a persistant storage volume inside the RSAT docker container.

Funding
This work was partly funded by the Spanish Ministry of Economy and Competitiveness grants AGL2014-52063R, AGL2017-83358-R (MCIU/AEI/FEDER/UE); and the Government of Aragón with grants A44 and A09_17R, which were co-financed with FEDER funds. N Ksouri was hired by project AGL2014-52063R and now funded by a PhD fellowship awarded by the Government of Aragón and co-financed with ESF funds respectively.