Additional file 8: of Putative bovine topological association domains and CTCF binding motifs can reduce the search space for causative regulatory variants of complex traits

Figure S1. Runs of genes with allele-specific expression within regulatory units. Only runs of genes within TAD and between CTCF binding motifs are shown. Our ANOVA models showed that both TAD and CTCF are significant factors (P-value ≤ 10−6 and false discovery rate < 0.01) explaining the observed ASE variation, while gene is a also a significant factor in Figure S1A but not a significant factor in Figure S1B. The ASE scores (y-axis) for heterozygous loci (x-axis) are plotted as black dot points in each Manhattan plot. Since ASE score was a division of paternal to maternal allelic read counts, the heterozygous locus whose ASE score is larger than 0 favours paternal expression, and the heterozygous locus whose ASE score is less than 0 favours maternal expression. The putative bovine TAD is represented as a rectangle centring at y = 0. The CTCF binding motifs (motif score ≥ 80 and motif P-value ≤ 10−8) are represented as the start and end position of each arrowed curve, where the direction of the arrow is the direction of transcription. Genes are represented as coloured bars starting from y = 0 towards either the top (gene on forward strand) or the bottom (gene on reverse strand) of the graph. Gene names or IDs from Ensembl UMD3.1 annotation (release 75) are listed in legend. (ZIP 260 kb)

补充图S1. 调控单元内携带等位基因特异性表达（Allele-Specific Expression, ASE）的基因连续区段。仅展示位于拓扑关联结构域（Topologically Associating Domain, TAD）内且处于CTCF结合基序之间的基因区段。本研究的方差分析（Analysis of Variance, ANOVA）模型表明，TAD与CTCF均为解释观测到的ASE变异的显著影响因素（P值≤10⁻⁶，错误发现率<0.01）；其中在补充图S1A中，基因同样为显著影响因素，但在补充图S1B中则不具备显著影响效应。
本研究将杂合位点（横轴）的ASE得分（纵轴）以黑色散点形式绘制于各曼哈顿图中。由于ASE得分是父本与母本等位基因测序读段计数的比值，因此ASE得分大于0的杂合位点倾向于父本表达，而ASE得分小于0的杂合位点倾向于母本表达。
推定的牛TAD以y=0为中心的矩形表示。CTCF结合基序（基序得分≥80且基序P值≤10⁻⁸）以各箭头曲线的起止位置标注，箭头方向即为转录方向。基因以从y=0向图像上方（正链基因）或下方（负链基因）延伸的彩色条带表示。图例中标注了来自Ensembl UMD3.1注释（版本75）的基因名称或ID。（ZIP 260 kb）