GeneExpressionProfiling

1. Landscape of gene expression of Tomato.
2. Genotype and tissue specific heat responsive genes patterns
3. Candidate gene selection
4. Co-expression of candidate genes for their co regulation
5. Conserved candidate genes selection by phylogenetic profiling
6. Functional characterization of candidate genes

Features

RNA samples collected from GEO with a diverse combination of

1. 17 genotypes of Tomato
2. 7 tissue types
3. 3 level of heat treatments with respective controls
4. Different duration of heats

inputs/master.table.csv contains all details information of samples, SRA, genotype, tissues and stress.

Downloading, quality checking and mapping was done by using https://github.com/NAMlab/rnaseq-mapper tool.

Co-evolution profil was analysed by following Hogprof (https://github.com/DessimozLab/HogProf) and OMA browser.

If you have any questions please feel free to contact with me [email protected] (Abul Khayer)