Table 1.

Key Points of Publications Assessing Sex-Biased Gene Expression.

Reference	donor or sample numbers (% male)1	n samples/tissue males	n samples/tissue females	n tissues	Data source	cutoff for differential expression	primary assessment (Table 2)	total genes analyzed	total sex-biased genes	% genes sex-biased in 1 or more tissues
(Mele et al., 2015)	175 donors (63%)	14–99	11–57	43	GTEx pilot set	False discovery rate (FDR) <0.05	Any gene with sex bias	20,110 protein or non-coding genes	753 (mostly breast)	0.1– 0.23% per tissue
(Mayne et al., 2016)	2500 samples (68%)	5–622	7–289	15	Compiled microarray data	FDR < 0.05	Any gene with sex bias	not directly provided	163–1818 genes	32% autosomal
(Gershoni & Pietrokovski, 2017)	544 donors (64%)	Number of samples per tissue not specified	NA	45	GTEx v6	p <0.05, fold change ≥ 2	Any gene with sex bias, excluded mammary gland	18,670 protein coding genes only	“just over” 6500	35% total
(Tukiainen et al., 2017)	449 donors (65%)	43–228	26–133	29	GTEx v6	FDR < 0.01	Any X chromosome gene with sex bias, excluded mammary gland	681 protein-coding or long non-coding genes on the X chromosome		4% inactivated, 6% variable inactivation, 48% escape genes
(Naqvi et al., 2019)	740 samples selected (67%)	17–83	9–36	12	GTEx v6p	≥ 1.05 fold change in 4/5 species	Any gene with sex bias conserved across mammals	12,939 protein-coding orthologs only	3161	24% total
(Kassam et al., 2019)	617 donors (73%)	80–491	23–125	40	GTEx v7	Bonferroni corrected significance threshold of PTSSD≤1.58×10−6	Any gene with sex bias, excluded mammary, pituitary, and minor salivary glands	23,608 mean protein or non-coding genes per tissue	131 per tissue	0.6 % per tissue
(Lopes-Ramos et al., 2020)	548 donors (66%)	82–290	36–162	29	GTEx v6	FDR <0.05, fold change ≥ 1.5	Any gene predicted to be targeted by sex-biased gene regulatory network	30,243 protein or non-coding genes	Overall median 64 differentially expressed genes per tissue (4,181 in breast); overall median 169 differentially targeted per tissue (25,994 in breast)	0.2 % differentially expressed per tissue; 0.6 % differentially targeted per tissue
(Oliva et al., 2020)	838 donors (61–78%)	78–469	33–237	44	GTEx v82	Local False Sign Rate (LFSR) ≤ 0.05	Any gene with sex bias	35,431 protein or non-coding genes	473 to 4558 per tissue	1.3% to 12.9% per tissue
(Hartman et al., 2020)	14 boy-girl newborn twins (50%), 172 adult (75%)	7/newborn, 129/adult	7/newborn, 43/adult	2	Newborns: RNA seq, Adults: microarray GSE30169	“intrinsic” p-value < 0.1 at birth and < 0.05 in adults; “acquired” p-value > 0.5 at birth and < 0.05 in adults; any fold change	Any gene with sex bias in HUVEC or HAEC3	18630 protein or non-coding genes (same genes queried in RNA seq & microarray)	2528 at birth in boy/girl twins, 1,798 in adults, 268 in both	25% of newborn and 14% of adult EC transcriptome
(Hartman, Mokry, et al., 2021)	>700 donors (59–69%)	116–538	82–256	24	GTEx v8	FDR<0.1, fold change ≥ 2 with coexpression in more than 20 permutations of the data	Any gene with sex bias. More than 80 samples of each type and sex	13,787 protein or non-coding genes	4062	29.5% total

¹The papers varied widely in how sample numbers were reported. The numbers, if present, were often buried deeply in supplemental files.

²v8 is the latest GTEx Release (dbGaP Accession phs000424.v8.p2) with 54 tissues from 636 male and 312 female donors (85% white). Details are here: https://www.gtexportal.org/home/tissueSummaryPage

³HUVEC: human umbilical vein endothelial cells; HAEC: human adult aortic endothelial cells