Supplementary Information for the manuscript: "Gene expression evolution is predicted by stronger selection at more pleiotropic genes"

<p>This repository contains the supplementary information for the manuscript "<em>Gene expression evolution is predicted by stronger selection at more pleiotropic genes</em>" (<a href="https://doi.org/10.1101/2024.07.22.604294">https://doi.org/10.1101/2024.07.22.604294</a>).</p> <p>The supplementary data "data.tar.gz" is related to the Github repository <a href="https://github.com/charlesrocabert/Koch-et-al-Gene-expression-evolution-is-predictable-and-driven-by-indirect-selection-pressures">https://github.com/charlesrocabert/Koch-et-al-Predictability-of-Gene-Expression</a>.</p> <h2>Content of the repository</h2> <ul> <li><strong>Script S1. </strong>BSFG estimates (50.9 MB).</li> <li><strong>Script S2.</strong>&nbsp;WGCNA analysis and results G1 (99.6 MB).</li> <li><strong>Data S1.</strong> Datasets resulting from the global genomics analysis of the output of the transcriptomics pipeline (5.9 MB).</li> <li><strong>Data S2.</strong> VCF file containing the 566,296 quality-checked SNPs (1.1 GB).</li> <li><strong>Data S3.</strong> VCF file containing the 358,142 SNPs with a call rate higher or equal to 50% (964.3 MB).</li> <li><strong>Data S4.</strong> VCF file containing the imputed genotypes (964.3 MB).</li> <li><strong>Data S5.</strong> Results of the imputation tests (479.5 kB).</li> <li><strong>Data S6.</strong> 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).</li> <li><strong>Data S7.</strong> List of the 1,273 significant eQTL associations (for gene expression levels or relative fitness as phenotypes) (61.2 kB).</li> <li><strong>Data S8.</strong> 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).</li> <li><strong>Data S9.</strong> List of all SNPs indicating if their AFC is significantly higher in each line and their degree of parallelism (2.4 MB).</li> <li><strong>Data S10.</strong> Excel file containing the results of the gene functional enrichment analysis of the hub and eQTL carrier genes (33.7 KB).</li> <li><strong>data.tar.gz.</strong> Dataset mandatory to re-run the genomics analysis (see <a href="https://github.com/charlesrocabert/Koch-et-al-Gene-expression-evolution-is-predictable-and-driven-by-indirect-selection-pressures">https://github.com/charlesrocabert/Koch-et-al-Predictability-of-Gene-Expression</a>) (7.8 GB).</li> </ul> <p>&nbsp;</p>