eQTLus-Maximus

Here presented is my minor project for the MCLS master of UU. It was a metanalysis on transcriptomic data of A. thanliana studies obtained from AraQTL. The project was done under the supervision of Basten Snoek from Utrecht University’s bioinformatics department. The script here presented is an edited version of a script authored by Margi Hartanto (2020), presented in his pubbliaction: Network Analysis Prioritizes DEWAX and ICE1 as the Candidate Genes for Major eQTL Hotspots in Seed Germination of Arabidopsis thaliana. M. Hartanto authored this script specifically for the comparison of transcriptomic data obtained from seeds at different developmental stages. With some editing, here the script was repurposed for similar comparison of a cohort of datasets which covered an ample range of A. thaliana developmental stages and experimental conditions. My original script was also appended onto M. Hartanto’s script to focus the transcriptomic analysis towards the identification of corresponding eQTLs (here coined coreQTLs). CoreQTLs are those eQTLs which are found in multiple datasets from different studies and are both overlapping and share linked traits. The reason for identifying these eQTLs is that they may offer higher certainty to be the same eQTL acting in the same way in different lines and experimental setups, and not different neighboring eQTLs with different roles which are being incorrectly lumped together. The project as it stand now, is not completed, as the work to quantify the increase in in eQTL resolution has not been undertaken.