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

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

• 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