DOI: 10.5281/zenodo.2658829
title: Conservation, acquisition, and functional impact of sex-biased gene expression in mammalian tissues

description: Processed data and code for Sahin Naqvi, Alexander K. Godfrey, Jennifer F. Hughes, Mary L. Goodheart, Richard N. Mitchell, & David C. Page <br> <br> <strong>Conservation, acquisition, and functional impact of sex-biased gene expression in mammalian tissues</strong> Expression values gtex.filt.salmon.tximport.unadj.tpm.txt.gz Unadjusted TPM values for filtered GTEx samples gtex.filt.salmon.tximport.unadj.counts.txt.gz Unadjusted counts for filtered GTEx samples gtex.filt.salmon.tximport.adj.counts.txt.gz PCA- and histology-adjusted counts for filtered GTEx samples cyno.salmon.tximport.tpm.txt.gz Cynomolgus macaque TPM values cyno.salmon.tximport.counts.txt.gz Cynomolgus macaque counts mouse.salmon.tximport.tpm.txt.gz Mouse TPM values mouse.salmon.tximport.counts.txt.gz Mouse counts rat.salmon.tximport.tpm.txt.gz Rat TPM values rat.salmon.tximport.counts.txt.gz Rat counts dog.salmon.tximport.tpm.txt.gz Dog TPM values dog.salmon.tximport.counts.txt.gz Dog counts Metadata human.metadata.txt Human metadata (abbreviated version of GTEx metadata) histeval.rds Novel histological evaluations for 6 tissues (.rds file to read into R) nonhuman.metadata.txt Non-human metadata Scripts filterSamples.R R code to filter GTEx samples based on medical history and cause of death cadjust_exprvals.Rmd R code to perform PCA and histology-based adjustment of expression values in GTEx data choosePCs.R Helper function for 'pcadjust_exprvals.Rmd' perform_sexdiff.Rmd R code to perform linear modeling of sex differences across 12 tissues and 5 species. Uses 'getSexBiasStats.R' getSexBiasStats.R Helper function for 'perform_sexdiff.Rmd' Intermediate files one2oneorth_emblids.txt One-to-one orthologs across the 5 species one2oneorth_60spectis_beta.txt Gene x tissue-species matrix of estimates of sex bias (beta) one2oneorth_60spectis_beta_se.txt Gene x tissue-species matrix of estimates of sex bias (beta) standard error one2oneorth_60spectis_mashr_pm.txt Gene x tissue-species matrix of mashr posterior estimates of sex bias (posterior mean) one2oneorth_60spectis_mashr_lfsr.txt Gene x tissue-species matrix of mash local false sign rate salmon.starref.tximport.voom.spec5orth.sfa_F.out Sparse factors learned from the gene x tissue-species beta matrix, used as input to mashr Output files sexbias.conserved.matrix.txt Gene x tissue matrix of conserved sex bias. 1 indicates male bias, -1 female bias (same for other matrices in this section) sexbias.primategain.matrix.txt Gene x tissue matrix of sex bias gained in primates sexbias.primateloss.matrix.txt Gene x tissue matrix of sex bias lost in primates sexbias.rodentgain.matrix.txt Gene x tissue matrix of sex bias gained in rodents sexbias.rodentloss.matrix.txt Gene x tissue matrix of sex bias lost in rodents sexbias.humangain.matrix.txt Gene x tissue matrix of sex bias gained in human sexbias.cynogain.matrix.txt Gene x tissue matrix of sex bias gained in cyno sexbias.mousegain.matrix.txt Gene x tissue matrix of sex bias gained in mouse sexbias.ratgain.matrix.txt Gene x tissue matrix of sex bias gained in rat sexbias.doggain.matrix.txt Gene x tissue matrix of sex bias gained in dog sexbias.multiplegain.matrix.txt Gene x tissue matrix of sex bias likely gained in multiple lineages sexbias.multipleloss.matrix.txt Gene x tissue matrix of sex bias likely lost in multiple lineages sexbias.complex.matrix.txt Gene x tissue matrix of sex bias with complex patterns across species that could not be categorized into gains or losses Data from other studies liang2017.human.skin.txt Limma/voom output of sex differences in human skin, from Liang et al, 2017 lindholm2017.human.muscle.txt Limma/voom output of sex differences in human muscle, from Lindholm et al, 2017 li2017.marin2017.mouse.heart.txt Limma/voom output of sex differences in mouse heart, combining Li et al, 2017 and Marin et al, 2017 li2017.marin2017.mouse.liver.txt Limma/voom output of sex differences in mouse liver, combining Li et al, 2017 and Marin et al, 2017 li2017.mouse.adrenal.txt Limma/voom output of sex differences in mouse adrenal gland, from Li et al, 2017 li2017.mouse.brain.txt Limma/voom output of sex differences in mouse brain, from Li et al, 2017 li2017.mouse.lung.txt Limma/voom output of sex differences in mouse lung, from Li et al, 2017 li2017.mouse.muscle.txt Limma/voom output of sex differences in mouse muscle, from Li et al, 2017 li2017.mouse.spleen.txt Limma/voom output of sex differences in mouse spleen, from Li et al, 2017 yang2006.mouse.muscle.geo2r.txt GEO2R output of sex differences in mouse muscle, from Yang et al, 2006 franco2010.mouse.lung.geo2r.txt Lim GEO2R output of sex differences in mouse lung, from Franco et al, 2010