Supplementary material - Co-expression pan-network reveals genes involved in complex traits within maize pan-genome

<strong>Additional Data</strong> <strong>Additional file 1: Table S1</strong> <strong>Title: Table S1. </strong>GWAS-hits within genes and promoters (TPM&gt;5 median) <strong>Description:</strong> The number of nodes and edges for each NAM genotype are presented for the GWAS-driven co-expression network. <br> <strong>Additional file 2: Data S1</strong> <strong>Title: Dataset S1. </strong>The number of edges shared by the number of lines. <strong>Description:</strong> The column "number of lines" represent the number of co-expressed gene-pairs (edges) observed in the number of lines. For example, the 5th row represents the unique gene-pairs for each genome whereas the row 30th represent the gene-pairs observed in all 26 NAM genomes. <br> <strong>Additional file 3: Data S2</strong> <strong>Title: Dataset S2. </strong>Enriched GO terms in pan-network sub-categories <strong>Description:</strong> Enriched GO terms in pan-network sub-categories <br> <strong>Additional file 4: Table S2</strong> <strong>Title: Table S2. </strong>genic vs genic/promoter network stats <strong>Description:</strong> The number of nodes and edges within the pan-network categories for the GWAS hits overlapping the genic regions only and overlapping either genic or promoter regions. <br> <strong>Additional file 5: Data S3</strong> <strong>Title: Dataset S3</strong>. The distribution of 41 complex traits within the genic and genic/promoter networks <strong>Description:</strong> The counts and percentages of the trait-associated SNPs overlapping the genic regions and genic/promoter regions. <br> <strong>Additional file 6: Data S4</strong> <strong>Title: Dataset S4.</strong> GO term enrichment in the genic and genic/promoter networks <strong>Description:</strong> GO term enrichment in the genic and genic/promoter networks <br> <strong>Additional file 7: Data S5</strong> <strong>Title: Dataset S5. </strong>The data for individual pan-networks for 41 traits separately <strong>Description:</strong> The co-expressed gene pairs (gene1 and gene2) and the list of traits associated with these genes (trait1 and trait2, respectively) are presented together with the NAM genomes co-expressing the both genes and the pan-network sub-category. <br> <strong>Additional file 8: Data S6</strong> <strong>Title: Dataset S6. </strong>Starch associated genes and annotations <strong>Description:</strong> The annotation of the genes involved in the Starch pan-network <br> <strong>Additional file 9: Data S7</strong> <strong>Title: Dataset S7. </strong>Matrix of GWAS SNP positions in each genome <strong>Description:</strong> The Wallace GWAS SNPs mapped to each of the 26 NAM genomes