Microarray data analysis of the shade avoidance in plants

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Background: When young plant seedling are in the shade, they will tend to elongate in order to rise above neighboring plants that may be shading it. This is part of the "Shade Avoidance Response" which provides the plant with a competitive advantage.

Goal: The Fankhauser lab at CIG (UNIL) has microarray expression data of plants grown in a shaded or unshaded environments, for various shade avoidance mutants. The goal of this project is to analyse this data and compare the results to similar publicly available data recenty reported in the scientific literature.

Mathematical tools: Statistics. The students will learn the basics of microarray data analysis using the R software.

Biological or Medical aspects: The regulation of the shade avoidance response in Arabidopsis thaliana.

Supervisor: Micha Hersch

Students: Alain Reymond, Patrice Descombes & Marie-Aude Tschopp



  1. Lorrain S, Trevisan M, Pradervand S, and Fankhauser C. Phytochrome interacting factors 4 and 5 redundantly limit seedling de-etiolation in continuous far-red light. Plant J 2009 Nov; 60(3) 449-61. doi:10.1111/j.1365-313X.2009.03971.x pmid:19619162. PubMed HubMed [lorrain09]
  2. Leivar P, Tepperman JM, Monte E, Calderon RH, Liu TL, and Quail PH. Definition of early transcriptional circuitry involved in light-induced reversal of PIF-imposed repression of photomorphogenesis in young Arabidopsis seedlings. Plant Cell 2009 Nov; 21(11) 3535-53. doi:10.1105/tpc.109.070672 pmid:19920208. PubMed HubMed [quai]
All Medline abstracts: PubMed HubMed

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