Processed data and code

Processed data and code for

Sahin Naqvi, Alexander K. Godfrey, Jennifer F. Hughes, Mary L. Goodheart, Richard N. Mitchell, & David C. Page

Conservation, acquisition, and functional impact of sex-biased gene expression in mammalian tissues

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

sexbias.conserved.lmm.log2fc.txt Gene x tissue matrix of estimates of conserved sex bias (beta output from linear mixed model)
sexbias.conserved.lmm.pval.txt Gene x tissue matrix of p-values for conserved sex bias (from linear mixed model)
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_beta.txt Gene x tissue-species matrix of mashr posterior estimates of sex bias (posterior mean)
one2oneorth_60spectis_beta_se.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.corrected.12.13.19.txt Gene x tissue matrix of sex bias likely lost in multiple lineages. CORRECTED ON 12/12/19
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