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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 <ul> <li>gtex.filt.salmon.tximport.unadj.tpm.txt.gz Unadjusted TPM values for filtered GTEx samples</li> <li>gtex.filt.salmon.tximport.unadj.counts.txt.gz Unadjusted counts for filtered GTEx samples</li> <li>gtex.filt.salmon.tximport.adj.counts.txt.gz PCA- and histology-adjusted counts for filtered GTEx samples</li> <li>cyno.salmon.tximport.tpm.txt.gz Cynomolgus macaque TPM values</li> <li>cyno.salmon.tximport.counts.txt.gz Cynomolgus macaque counts</li> <li>mouse.salmon.tximport.tpm.txt.gz Mouse TPM values</li> <li>mouse.salmon.tximport.counts.txt.gz<a href="http://pagelab.wi.mit.edu/page/papers/Naqvi_et_al_2019/exprvals/mouse.salmon.tximport.counts.txt.gz"> </a>Mouse counts</li> <li>rat.salmon.tximport.tpm.txt.gz Rat TPM values</li> <li>rat.salmon.tximport.counts.txt.gz Rat counts</li> <li>dog.salmon.tximport.tpm.txt.gz Dog TPM values</li> <li>dog.salmon.tximport.counts.txt.gz Dog counts</li> </ul> Metadata <ul> <li>human.metadata.txt Human metadata (abbreviated version of GTEx metadata)</li> <li>histeval.rds Novel histological evaluations for 6 tissues (.rds file to read into R)</li> <li>nonhuman.metadata.txt Non-human metadata</li> </ul> Scripts <ul> <li>filterSamples.R<a href="http://pagelab.wi.mit.edu/page/papers/Naqvi_et_al_2019/scripts/filterSamples.R"> </a>R code to filter GTEx samples based on medical history and cause of death</li> <li>cadjust_exprvals.Rmd<a href="http://pagelab.wi.mit.edu/page/papers/Naqvi_et_al_2019/scripts/pcadjust_exprvals.Rmd"> </a>R code to perform PCA and histology-based adjustment of expression values in GTEx data</li> <li>choosePCs.R<a href="http://pagelab.wi.mit.edu/page/papers/Naqvi_et_al_2019/scripts/choosePCs.R"> </a>Helper function for 'pcadjust_exprvals.Rmd'</li> <li>perform_sexdiff.Rmd R code to perform linear modeling of sex differences across 12 tissues and 5 species. Uses 'getSexBiasStats.R'</li> <li>getSexBiasStats.R<a href="http://pagelab.wi.mit.edu/page/papers/Naqvi_et_al_2019/scripts/getSexBiasStats.R"> </a>Helper function for 'perform_sexdiff.Rmd'</li> </ul> Intermediate files <ul> <li>one2oneorth_emblids.txt One-to-one orthologs across the 5 species</li> <li>one2oneorth_60spectis_beta.txt Gene x tissue-species matrix of estimates of sex bias (beta)</li> <li>one2oneorth_60spectis_beta_se.txt Gene x tissue-species matrix of estimates of sex bias (beta) standard error</li> <li>one2oneorth_60spectis_mashr_pm.txt Gene x tissue-species matrix of mashr posterior estimates of sex bias (posterior mean)</li> <li>one2oneorth_60spectis_mashr_lfsr.txt Gene x tissue-species matrix of mash local false sign rate</li> <li>salmon.starref.tximport.voom.spec5orth.sfa_F.out Sparse factors learned from the gene x tissue-species beta matrix, used as input to mashr</li> </ul> Output files <ul> <li>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)</li> <li>sexbias.primategain.matrix.txt Gene x tissue matrix of sex bias gained in primates</li> <li>sexbias.primateloss.matrix.txt<a href="http://pagelab.wi.mit.edu/page/papers/Naqvi_et_al_2019/sexbias.primateloss.matrix.txt"> </a>Gene x tissue matrix of sex bias lost in primates</li> <li>sexbias.rodentgain.matrix.txt Gene x tissue matrix of sex bias gained in rodents</li> <li>sexbias.rodentloss.matrix.txt Gene x tissue matrix of sex bias lost in rodents</li> <li>sexbias.humangain.matrix.txt Gene x tissue matrix of sex bias gained in human</li> <li>sexbias.cynogain.matrix.txt Gene x tissue matrix of sex bias gained in cyno</li> <li>sexbias.mousegain.matrix.txt Gene x tissue matrix of sex bias gained in mouse</li> <li>sexbias.ratgain.matrix.txt Gene x tissue matrix of sex bias gained in rat</li> <li>sexbias.doggain.matrix.txt Gene x tissue matrix of sex bias gained in dog</li> <li>sexbias.multiplegain.matrix.txt Gene x tissue matrix of sex bias likely gained in multiple lineages</li> <li>sexbias.multipleloss.matrix.txt Gene x tissue matrix of sex bias likely lost in multiple lineages</li> <li>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</li> </ul> Data from other studies <ul> <li>liang2017.human.skin.txt Limma/voom output of sex differences in human skin, from Liang et al, 2017</li> <li>lindholm2017.human.muscle.txt Limma/voom output of sex differences in human muscle, from Lindholm et al, 2017</li> <li>li2017.marin2017.mouse.heart.txt Limma/voom output of sex differences in mouse heart, combining Li et al, 2017 and Marin et al, 2017</li> <li>li2017.marin2017.mouse.liver.txt Limma/voom output of sex differences in mouse liver, combining Li et al, 2017 and Marin et al, 2017</li> <li>li2017.mouse.adrenal.txt Limma/voom output of sex differences in mouse adrenal gland, from Li et al, 2017</li> <li>li2017.mouse.brain.txt Limma/voom output of sex differences in mouse brain, from Li et al, 2017</li> <li>li2017.mouse.lung.txt Limma/voom output of sex differences in mouse lung, from Li et al, 2017</li> <li>li2017.mouse.muscle.txt Limma/voom output of sex differences in mouse muscle, from Li et al, 2017</li> <li>li2017.mouse.spleen.txt Limma/voom output of sex differences in mouse spleen, from Li et al, 2017</li> <li>yang2006.mouse.muscle.geo2r.txt GEO2R output of sex differences in mouse muscle, from Yang et al, 2006</li> <li>franco2010.mouse.lung.geo2r.txt Lim GEO2R output of sex differences in mouse lung, from Franco et al, 2010</li> </ul>

ShareScore

24/100

Overall dataset sharing score

Score breakdown

These five areas show where the dataset supports — or may limit — practical reuse.

Stewardship: 4
Harmonization: 4
Access: 16
Reuse readiness: 0
Engagement: 0