Additional file 2: Table S1. of Regulatory and evolutionary signatures of sex-biased genes on both the X chromosome and the autosomes
Creators: name: Jiangshan Shen
name: Wang, Ting-You
name: Wanling Yang
Publisher: name: Figshare
Year: 2017
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Sociology
subject: FOS: Sociology
subject: FOS: Sociology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Mental Health
subject: Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: Computational Biology

description: Linear regression of dN/dS, or the amount of selection pressure, as a function of the following variables. Estimate refers to the coefficient of the covariate, Std.Error referes to the standard error of that estimate. T value refers to the test statistic of the estimate and Pr(&gt;|t|) refer to the P value of that covariate. XYpair refers to whether the gene is part of an XY homologous pair. XAR or XCR refers to whether the gene belongs on the X added region on the X chromosome or the X conserved region strata, escape status refers to whether the gene is classified as an escape gene, and gene expression refers to the average level of gene expression among 264 female samples. Table S2. Linear regression of dN/dS, or the amount of selection pressure, as a function of the following variables. Estimate refers to the coefficient of the covariate, Std.Error referes to the standard error of that estimate. T value refers to the test statistic of the estimate and Pr(&gt;|t|) refer to the p value of that covariate. Average gene expression refers to average level of gene expression among 462 samples. Gene bias_female refers to whether the gene is classified as female-biased, and the coefficient refers to the change in dnds between female-biased genes to genes without sex bias. Gene bias_male refers similarly to genes classified as male-biased. Gene expression breadth refers to the number of tissues the gene is expressed in. Table S3. Sex-biased genes (sDEG) (587 genes) from LCL data and GTex data (1308) and their relationship to replication timing data in different cell lines, based on the Spearman’s Rho between replication timing values and log2fc of gene expression between females and males. Table S4(a). GSEA results for gene regions that are enriched in female biased sDEGs. Table S4(b). ToppFun results for gene regions that are enriched in male-biased sDEGs. Table S5(a). Disease gene sets enriched in sex biased genes, as found by ToppFun. Table S5(b). GO terms enriched in sex biased genes, as found by ToppFun. Table S5 (c). Pubmed gene sets enriched in sex biased genes, as found by ToppFun. Table S5 (d). Pathway analysis of sex biased genes using gene sets from MSigDBC2, as found by ToppFun. Table S5 (e). Gene families enriched in sex biased genes, as found by ToppFun. Table S6 (a). Domains enriched in female biased genes, as found by ToppFun. Table S6 (b). KEGG pathways enriched in female biased genes, as found by GSEA. Table S7. Pathway analysis of sex biased genes in GSEA, using custom gene sets from [26–28, 43]. Table S8 (a). Gene families enriched in male biased genes. Table S8 (b). MSigDB gene sets enriched in male biased genes, as found by ToppFUn. Table S9. Pathways enriched in transcription factors enriched for female biased genes. (DOCX 49 kb)