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

NIAID Data Ecosystem2026-03-14 收录

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Additional Data Additional file 1: Table S1 Title: Table S1. GWAS-hits within genes and promoters (TPM>5 median) Description: The number of nodes and edges for each NAM genotype are presented for the GWAS-driven co-expression network. Additional file 2: Data S1 Title: Dataset S1. The number of edges shared by the number of lines. Description: 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. Additional file 3: Data S2 Title: Dataset S2. Enriched GO terms in pan-network sub-categories Description: Enriched GO terms in pan-network sub-categories Additional file 4: Table S2 Title: Table S2. genic vs genic/promoter network stats Description: 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. Additional file 5: Data S3 Title: Dataset S3. The distribution of 41 complex traits within the genic and genic/promoter networks Description: The counts and percentages of the trait-associated SNPs overlapping the genic regions and genic/promoter regions. Additional file 6: Data S4 Title: Dataset S4. GO term enrichment in the genic and genic/promoter networks Description: GO term enrichment in the genic and genic/promoter networks Additional file 7: Data S5 Title: Dataset S5. The data for individual pan-networks for 41 traits separately Description: 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. Additional file 8: Data S6 Title: Dataset S6. Starch associated genes and annotations Description: The annotation of the genes involved in the Starch pan-network Additional file 9: Data S7 Title: Dataset S7. Matrix of GWAS SNP positions in each genome Description: The Wallace GWAS SNPs mapped to each of the 26 NAM genomes

附加数据附加文件1：表S1 标题：表S1. 基因及启动子区域内的全基因组关联分析（GWAS, Genome-Wide Association Study）命中位点（中位TPM>5）描述：本文件展示了全基因组关联分析驱动的共表达网络中，各NAM基因型对应的节点与边的数量。附加文件2：数据集S1 标题：数据集S1. 由品系数目共享的边的数量描述：其中“品系数目”列代表在对应数量的品系中观测到的共表达基因对（即边）的数量。例如，第5行对应每个基因组的独有基因对，而第30行对应在全部26个NAM基因组中均观测到的基因对。附加文件3：数据集S2 标题：数据集S2. 泛网络子类别中的富集GO术语描述：泛网络子类别中的富集基因本体（GO, Gene Ontology）术语。附加文件4：表S2 标题：表S2. 基因区域vs基因/启动子区域网络统计描述：本文件展示了仅重叠基因区域、以及重叠基因区域或启动子区域的GWAS命中位点在各泛网络类别中的节点与边的数量。附加文件5：数据集S3 标题：数据集S3. 基因区域及基因/启动子区域网络内41个复杂性状的分布描述：重叠于基因区域与基因/启动子区域的性状关联单核苷酸多态性（SNP, Single Nucleotide Polymorphism）的计数与占比情况。附加文件6：数据集S4 标题：数据集S4. 基因区域及基因/启动子区域网络中的GO术语富集分析结果描述：基因区域及基因/启动子区域网络中的基因本体（GO）术语富集分析结果。附加文件7：数据集S5 标题：数据集S5. 41个性状各自的独立泛网络数据描述：本文件展示了共表达基因对（基因1与基因2），以及与这些基因相关的性状列表（分别为性状1与性状2），同时包含共表达这两个基因的NAM基因组，以及对应的泛网络子类别。附加文件8：数据集S6 标题：数据集S6. 淀粉相关基因及其注释信息描述：参与淀粉泛网络的基因的注释信息。附加文件9：数据集S7 标题：数据集S7. 各基因组内的GWAS SNP位点矩阵描述：华莱士全基因组关联分析（Wallace GWAS）的单核苷酸多态性位点定位至全部26个NAM基因组的结果。

创建时间：

2022-10-19