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

This 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).本仓库包含手稿《多效基因上的更强选择可预测基因表达演化（Gene expression evolution is predicted by stronger selection at more pleiotropic genes）》的补充信息，该手稿DOI为：10.1101/2024.07.22.604294。 补充数据集“data.tar.gz”关联的GitHub仓库地址为https://github.com/charlesrocabert/Koch-et-al-Predictability-of-Gene-Expression。 本仓库内容如下： 附录S1：基于Beagle-5.4软件对原始VCF（Variant Call Format）文件开展的基因型填充质量测试（82.9 MB） 脚本S1：BSFG估计值（50.9 MB） 脚本S2：加权基因共表达网络分析（Weighted Gene Co-expression Network Analysis, WGCNA）及结果G1（99.6 MB） 数据S1：转录组分析流程输出结果的全局基因组学分析所得数据集（5.9 MB） 数据S2：包含566296个经过质量校验的单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）的VCF文件（1.1 GB） 数据S3：包含358142个分型调用率≥50%的SNPs的VCF文件（964.3 MB） 数据S4：包含填充后基因型的VCF文件（964.3 MB） 数据S5：基因型填充测试结果（479.5 kB） 数据S6：过滤掉次要等位基因频率（Minor Allele Frequency, MAF）<0.05的SNPs后的填充基因型VCF文件（MAF ≤0.05）（176.0 MB） 数据S7：1273个显著表达数量性状位点（expression Quantitative Trait Locus, eQTL）关联列表（以基因表达水平或相对适合度为表型）（61.2 kB） 数据S8：高密度（High-Density, HD）环境下，各遗传标记在品系L1、L2、L3、L5、L6、Mx1及Mx2中的等位基因频率变化（Allele Frequency Change, AFC）列表（32.4 MB） 数据S9：所有SNPs的列表，用于标注各品系中其AFC是否显著升高，及其平行演化程度（2.4 MB） 数据S10：包含枢纽基因及携带eQTL的基因的功能富集分析结果的Excel文件（33.7 KB） data.tar.gz：用于复现基因组学分析的必需数据集（详见https://github.com/charlesrocabert/Koch-et-al-Predictability-of-Gene-Expression）（7.8 GB）