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286 results for “sex expression”
Conservation, acquisition, and functional impact of sex-biased gene expression in mammalian tissues
<p>Processed data and code for</p> <p>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></p> <p>Expression values</p> <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> <p>Metadata</p> <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> <p>Scripts</p> <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> <p>Intermediate files</p> <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> <p>Output files</p> <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> <p>Data from other studies</p> <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>
Sex Differences in Gene Expression in Human Adipose Tissue
ClinicalTrials.gov study NCT00677651. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Clinical Utility of an Age, Sex, and Gene Expression Score (ASGES or Corus CAD) in African American Patients.
ClinicalTrials.gov study NCT02405754. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Sex, Hormones and Identity Affect Nociceptive Expression
ClinicalTrials.gov study NCT05787470. IPD Sharing: UNDECIDED. Countries: 1. Publications: 0.
Contribution of germline to sex-biased expression in Drosophila melanogaster
GEO Series GSE11017. Drosophila melanogaster. 22 samples. Type: Expression profiling by array.
Peri-pubertal gonadotropin-releasing hormone agonist treatment affects sex-biased gene expression of amygdala in sheep
GEO Series GSE44202. Ovis aries. 56 samples. Type: Expression profiling by array.
Tlr9 expression protects against Tlr7-dependent exocrine gland and systemic disease manifestations in primary Sjögren’s disease in a sex-biased manner
GEO Series GSE292271. Mus musculus; blank sample. 32 samples. Type: Protein profiling by protein array.
Sex-based disparities in DNA methylation and gene expression in late-gestation mouse placentas
GEO Series GSE252281. Mus musculus. 6 samples. Type: Expression profiling by high throughput sequencing.
Differential gene expression is not required for facultative sex allocation: a transcriptome analysis of brain tissue in the parasitoid wasp Nasonia vitripennis.
GEO Series GSE105796. Nasonia vitripennis. 23 samples. Type: Expression profiling by high throughput sequencing.
Sex differences in the effects of caloric restriction (CR) on hepatic gene expression in mice
GEO Series GSE230402. Mus musculus. 22 samples. Type: Expression profiling by high throughput sequencing.
Effect of male sex-category on gene expression in the m. longissimus dorsi (LD) and m. semispinalis capitis (SSC)
GEO Series GSE183240. Sus scrofa. 6 samples. Type: Expression profiling by high throughput sequencing.
Sex-biased gene and microRNA expression in the developing mouse brain is associated with neurodevelopmental functions and neurological phenotypes
GEO Series GSE211816. Mus musculus. 12 samples. Type: Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing.
Data from: Extensive sex-specific nonadditivity of gene expression in Drosophila melanogaster
Open the record for dataset details and reuse information.
Translating ribosome affinity purification of Esr1+ neuronal populations to identify sex and estrus-stage differentially expressed genes
GEO Series GSE183092. Mus musculus. 36 samples. Type: Expression profiling by high throughput sequencing.
Population and sex differences in Drosophila melanogaster brain gene expression
GEO Series GSE40907. Drosophila melanogaster. 8 samples. Type: Expression profiling by high throughput sequencing.
Liver miRNA Expression during the Rat Life Span in both Sexes
GEO Series GSE65169. Rattus norvegicus. 88 samples. Type: Non-coding RNA profiling by array.
Uncoupling X chromosome number from sex determination separates contribution of sex and X dose to sex-biased gene expression in C. elegans
GEO Series GSE77794. Caenorhabditis elegans. 14 samples. Type: Expression profiling by high throughput sequencing.
Acute Aerobic Exercise Alters PBMC microRNA Expression: Insights into Sport- and Sex-Specific Variations
GEO Series GSE288760. Homo sapiens. 182 samples. Type: Non-coding RNA profiling by high throughput sequencing.
Converging Effects of Three Different Endocrine Disrupters on Sox and Pou Gene Expression in Developing Rat Hippocampus: Possible Role of microRNA in Sex Differences
GEO Series GSE180054. Rattus norvegicus. 66 samples. Type: Expression profiling by high throughput sequencing.
Organ-, sex-, and age-dependent patterns of endogenous LINE-1 mRNA expression at a single locus resolution
GEO Series GSE158831. Rattus norvegicus; Mus musculus. 80 samples. Type: Expression profiling by high throughput sequencing.
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