Matrix N, TEs vs promoters, 100kb-wide windows, hg38

Regulatory susceptibility matrix N, with rows as hg38 protein coding genes and columns as TE subfamilies. A TE is counted if it is found within 100kb of a gene promoter, strictly out of any promoter and any exon belonging to that gene. Since hg38 contains inflated SVA integrants, most of which small fragments unlikely to be of functional importance, we filtered out SVA integrants shorter than 200bp.

调控易感矩阵N，其行对应hg38参考基因组中的蛋白编码基因，列对应转座因子（Transposable Element, TE）亚家族。当转座因子位于某基因启动子上下游100kb范围内，且严格处于该基因自身的启动子与外显子区域之外时，将被纳入该矩阵的统计。由于hg38参考基因组中存在过度富集的SVA整合元件，其中多数为短小片段，大概率不具备功能重要性，因此我们过滤掉了长度小于200bp的SVA整合元件。