Pan-Gene Atlas: Gene Expression and eQTL Information in 327 Hexaploid Wheat Lines

<b>00.Pan_gene.atlas.mRNA.fa</b><b>:</b> FASTA sequences of the pan-gene atlas.<b>01.pan_gene_atlas.type.txt</b><b>: </b>A list of all representative gene IDs included in the pan-gene atlas, along with their classifications. <b>02.327sample.pan-gene_atlas.TPM.txt:</b> Gene expression matrix of the pan-gene atlas across 327 samples.<b>03.Orthogroups.GeneCount.tsv:</b> Orthogroups of homologous genes from 44 wheat genomes with different ploidy levels, including the number of genomes and genes in each Orthogroup.<b>03.Orthogroups.tsv:</b> A matrix listing gene IDs within each Orthogroup.<b>03.Orthogroups_UnassignedGenes.tsv:</b> A list of unique genes specific to different ploidy wheat genomes.<b>04.all.active-eQTG.txt: eQTL results (Type 1-1):</b> SNPs located in expressed genes (active-eQTGs) that are associated with variation in eGene expression levels at the population level.<b>04.eGene_active-eQTG.correlation.txt: eQTL results (Type 1–2):</b> Spearman correlation (|SCC| &gt; 0.3, p &lt; 0.05) between expression levels of active eQTGs and pan-gene atlas eGenes across different gene haplotypes (0 = reference, 1 = heterozygous, 2 = alternative).<b>04.active-eQTG.SCC0.3p0.05.txt : eQTL results (Type 1–3):</b> Associations in which the expression levels of active-eQTGs show a Spearman correlation coefficient (|SCC| &gt; 0.3, p &lt; 0.05) with pan-gene atlas eGenes under any gene haplotype.<b>04.inactive-eQTG.txt: eQTL results (Type 2): </b>SNPs located in non-expressed genomic regions (inactive-eQTGs) that are associated with eGene expression from the pan-gene atlas at the population level.<b>04.intergenic-eQTL.txt: eQTL results (Type 3):</b> SNPs located in intergenic regions (intergenic-eQTLs) that are associated with eGene expression variation from the pan-gene atlas.<b>05.only_introgression.1B1R.active-eQTG.txt:</b> Summary of active-eQTGs identified from 50 1RS.1BL introgression lines.<b>05.only_introgression.1B1R.inactive-eQTG.txt:</b> Summary of inactive-eQTGs identified from 50 1RS.1BL introgression lines.<b>05.only_introgression.1B1R.intergenic-eQTL.txt:</b> Summary of intergenic-eQTLs identified from 50 1RS.1BL introgression lines.<b>06.only_introgression.2D.active-eQTG.txt:</b> Summary of active-eQTGs identified from 49 chromsome 2D introgression lines.<b>06.only_introgression.2D.inactive-eQTG.txt: </b>Summary of inactive-eQTGs identified from 49 chromsome 2D introgression lines.<b>06.only_introgression.2D.intergenic-eQTL.txt: </b>Summary of intergenic-eQTLs identified from 49 chromsome 2D introgression lines.<b>07.only_introgression.timopheevii_5G.5B.active-eQTG.txt: </b>Summary of active-eQTGs identified from 74 timopheevii_5G.5B introgression lines.<b>07.only_introgression.timopheevii_5G.5B.inactive-eQTG.txt:</b> Summary of inactive-eQTGs identified from 74 timopheevii_5G.5B introgression lines.<b>07.only_introgression.timopheevii_5G.5B.intergenic-eQTL.txt:</b> Summary of intergenic-eQTLs identified from 74 timopheevii_5G.5B introgression lines.