cc-by-4.0Guillaume, Frédéric2025-04-292025-04-282025-04-28https://datakatalogi.helsinki.fi/handle/123456789/5346This repository contains the supplementary information for the manuscript "Gene expression evolution is predicted by stronger selection at more pleiotropic genes" (https://doi.org/10.1101/2024.07.22.604294). The supplementary data "data.tar.gz" is related to the Github repository https://github.com/charlesrocabert/Koch-et-al-Predictability-of-Gene-Expression. Content of the repository Appendix S1. Imputation quality testing with Beagle-5.4 software on the raw VCF file (82.9 MB). Script S1. BSFG estimates (50.9 MB). Script S2. WGCNA analysis and results G1 (99.6 MB). Data S1. Datasets resulting from the global genomics analysis of the output of the transcriptomics pipeline (5.9 MB). Data S2. VCF file containing the 566,296 quality-checked SNPs (1.1 GB). Data S3. VCF file containing the 358,142 SNPs with a call rate higher or equal to 50% (964.3 MB). Data S4. VCF file containing the imputed genotypes (964.3 MB). Data S5. Results of the imputation tests (479.5 kB). Data S6. VCF file containing imputed genotypes where SNPs with a minor allele frequency lower than 0.05 have been filtered out (MAF $\leq$ 0.05) (176.0 MB). Data S7. List of the 1,273 significant eQTL associations (for gene expression levels or relative fitness as phenotypes) (61.2 kB). Data S8. List of allele frequency changes (AFCs) for every markers in HD environment, for lines L1, L2, L3, L5, L6, Mx1 and Mx2 (32.4 MB). Data S9. List of all SNPs indicating if their AFC is significantly higher in each line and their degree of parallelism (2.4 MB). Data S10. Excel file containing the results of the gene functional enrichment analysis of the hub and eQTL carrier genes (33.7 KB). data.tar.gz. Dataset mandatory to re-run the genomics analysis (see https://github.com/charlesrocabert/Koch-et-al-Predictability-of-Gene-Expression) (7.8 GB).  dataset