These datasets are related to 'The pan-genome of Saccharomyces cerevisiae' (Li G., Ji B., and Nielsen J.). This deposition contains following datasets: (1) Genomes.tar.gz: a compressed file containing 1392 Saccharomyces cerevisiae genome assembles analyzed (2) genome_information_2.0.tsv: a tab-separated text file that contains the basic information of above genomes, including genomeSize, contigNums, N50, busco_C(%), busco_S(%), busco_D(%), busco_F(%), busco_M(%), busco_n, number_of_genes, number_of_partial_genes, download_from, Eco_Source, Ploidy, Aneuploidies. (3) ClusterFasta.tar.gz: a compressed file that contains a list of fasta files. Each fasta file contains protein sequences in a cluster. The name of the fasta file is the name of the representative sequence of that cluster. (4) sc_gene_cluster_info_0.7_v4.tsv: a tab-separated text file that contains the properties of gene clusters. (5) gene_presence_absence_v4.tsv: a tab-separated text file that contains the gene-presence/absence information. Each columns is a gene cluster. Each row is a genome. Y/N is used to present presence/absence. (6) gene_num_in_clusters_of_each_strain_v4.tsv: a tab-sparated text file that contains the gene number of each genome in each cluster (copy number). Each columns is a gene cluster. Each row is a genome. (7) feature_importances_cv5_pa_cnv.tsv: a tab-separated file that contains the feature importance from a random forest classifier in a 5-fold cross-validation approach. The classifier was trained on gene presence/absence table (PA) or copy number table (CNV). The columns 'pa_x' indicate the feature importance in each fold of cross-validation on PA dataset. The columns 'cnv_x' indicate the feature importance in each fold of cross-validation on CNV dataset.