Venn diagram, gene enrichment (GO) pathway analysis and KEGG analysis

Venn diagrams were prepared for overlapping genes considering a combination of three comparative light conditions at a time. Gene lists from the microarray data were sorted and used for plotting Venn diagram using a custom script for R [67] using packages gdata [68], Vennerable [69], gplots [70], RBGL [71] and graph [72]. The script is available online on GitHub https://github.com/debadutta-patra/Venn-Diagram. GO pathway analysis was performed using Panther Over-representation test and the annotation version is GO Ontology database. The FISHER test was used and the categorization of DEGs under different GO terms was done considering FDR < 0.05. The KEGG search and colour pathway analysis was performed considering only a small group of DEGs.