Additional file 1 of Hearing loss genes reveal patterns of adaptive evolution at the coding and non-coding levels in mammals

Additional file 1: Supp. Tables S1 to S10. Table S1. Initial screening of hearing loss genes (n = 420) for signatures of coding positive selection in the mammalian basal branch. Table S2. Extensive analysis of 58 candidate positively selected hearing loss genes obtained from initial screening. Table S3. Screening of coding positive selection in the human branch, using a background of primate species for our hearing loss database (n = 420). Table S4. Screening of non-coding acceleration in the mammalian and human branches. Table S5. Functional evidence of regulatory activity in non-coding accelerated elements in the mammalian and human branches. Table S6. Effect of variation in positively selected sites using human protein as reference. Table S7. Gene ontology analyses for mammal coding positive selected genes against the hearing loss database. Table S8. Gene ontology analyses for different sets of genes: non-coding elements in mammals (ncTSARs) vs. coding positive selection in mammals. Table S9. Information for candidate regulatory regions in hearing loss genes tested in enhancer assays in transgenic zebrafish. Table S10. Summary of distinct approaches performed to test the relative contribution of coding and non-coding elements for each hearing loss gene.

补充材料1：附表S1至S10。
表S1：针对哺乳动物基部分支（mammalian basal branch）编码区正选择（coding positive selection）特征的420个耳聋基因（hearing loss genes）的初步筛选（n=420）。
表S2：对初步筛选获得的58个候选正选择耳聋基因的全面分析。
表S3：以灵长类物种（primate species）为参照类群，针对本研究耳聋基因数据库（hearing loss database，n=420）中的人类分支开展编码区正选择筛选。
表S4：哺乳动物及人类分支的非编码加速演化（non-coding acceleration）筛选。
表S5：哺乳动物及人类分支中非编码加速演化元件（non-coding accelerated elements）的调控活性（regulatory activity）功能证据。
表S6：以人类蛋白质（human protein）为参照的正选择位点（positively selected sites）变异效应分析。
表S7：以耳聋基因数据库为参照的哺乳动物编码区正选择基因的基因本体分析（Gene ontology analyses）。
表S8：两组不同基因集的基因本体分析：哺乳动物非编码元件（ncTSARs）与哺乳动物编码区正选择基因。
表S9：在转基因斑马鱼（transgenic zebrafish）增强子活性检测实验（enhancer assays）中验证的耳聋基因候选调控区域信息。
表S10：针对各耳聋基因编码区与非编码区元件相对贡献的各类检测方法汇总。