Dynamics of the hypersensitive response

Cladosporum fulvum is a fungus infecting crops. In a recent study, a tomato expressing a fungal resistance gene and a receptor recognizing pathogen-secreted proteins was infected, and during the so-called hypersensitive response both RNA expression was measured over time using microarrays [1]. Moreover, metabolomics data was measured on the same samples.

In this project, the goal is to go beyond the initial analyses performed in [1]. In particular, we would like to learn more on the dynamics of the hypersensitive response by inferring regulatory networks (e.g. [2]), incorporating as much prior knowledge as possible.

[1] D.W. Etalo et al. (2013) System-wide hypersensitive response-associated transcriptome and metabolome reprogramming in tomato. Plant Physiology 162:1599-1617. [2] C. Roven and H.J. Bussemaker (2003) REDUCE: an online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data. Nucleic Acids Research 31(13):3487-90.

Used skills: Programming, statistics

Requirements: INF-22306 Programming in Python, SSB-30306Molecular systems biology, BIF-30806 Advanced bioinformatics