GeneExpressionProfiling

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

Quick start

Following the steps

For mac users, it is recommended to install xquartz (https://github.com/XQuartz/XQuartz/releases/download/XQuartz-2.8.1/XQuartz-2.8.1.dmg) for handling libraries , applications and to avoid long waiting time to create heatmaps.

1. $ git clone https://github.com/zitunstu24/GeneExpressionProfiling
2. $ cd GeneExpressionProfiling
3. $ Rscript packages.R
4. $ cd inputs
5. $ gunzip combined_abundance.tsv.gz
6. $ cd ../

We are ready to go

Then run scripts in terminal with Rscript (e.g Rscript 1_DEGs.R)

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 zitunstu24@gmail.com (Abul Khayer)