Additional file 4 of Integrated analysis of robust sex-biased gene signatures in human brain
Creators: name: Wapeesittipan, Pattama
name: Joshi, Anagha
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 4: Figure S1. Schematic diagram of the workflow including rank aggregation for sex-biased genes detection in this study. Figure S2. Principal component analysisplot of Y- chromosome genes expression for GSE8397, GSE12649, GSE17612, GSE44456, GSE30483 and GSE45642. Figure S3. The cutoff for coefficient of age and sex variables in section multiple regression analysis with age and sex as independent variable. Figure S4. The number of sex-biased genes in individual datasets, aggregated lists in AMY, CBC, CC, HIP, MED and OC. Figure S5. The number of sex-biased genes in individual datasets, aggregated lists in PL, STR, TC and THA. Figure S6. Plot of number of sex-biased genes in different number of brain samples. Figure S7. Fraction of sex-biased genes found at least in 40 species and 160 species. Figure S8. The number of overlapping sex-biased genes by number of datasets for AMY, CBC, CC, FC, HIP and MED. Figure S9. The number of overlapping sex-biased genes by number of datasets for OC, PL, STR, TC and THA. Figure S10. The number of par1 genes in male-biased genes and the number of XCI female-biased genes. Figure S11. Gene ontology enrichment analysis of sex-biased genes for biological process. The top 5 enrich terms across brain regions in female-biased genes and male-biased genes. Figure S12. Gene ontology enrichment analysis of sex-biased genes for cellular component. The top 5 enrich terms across brain regions in female-biased genes and male-biased genes. Figure S13. Gene ontology enrichment analysis of sex-biased genes for molecular functions. The top 5 enrich GO terms across brain regions in female-biased genes and male-biased genes. Figure S14. KEGG pathway enrichment analysis of sex-biased genes. The top 5 enrich GO terms across brain regions in female-biased genes and male-biased genes.Figure S15. GWAS catalog 2019 enrichment across brain regions in female-biased genes and male-biased genes. Figure S16. DisGeNET enrichment analysis of sex-biased genes across brain regions in female-biased genes and male-biased genes. Figure S17. The number of autism genes found in sex-biased genes. Autism genes come from SFARI database. Figure S18. DisGeNetenrichment of overlap sex-biased genes across FC,PL,TC and OC in female-biased genes and male-biasd genes. GWAS catalog 2019 enrichment analysis of overlap sex-biased genes across FC, PL, TC and OC in female-biased genes and male-biased genes. Figure S19. Gene-disease class heatmap of DisGeNET for overlap sex-biased gene lists of PL, FC, TC and OC. Diseases are grouped by the their MeSH disease classes. The color scale is related to the percentage of disease in each class. Figure S20. Tissue-specific enrichment analysisof female-biased genes and male-biased genes. Figure S21. Cell type enrichment of sex-biased genes from McKenzie et al gene sets. Figure S22. Cell type specific expression analysisof female biased genes in AMY, CBC, CC, FC, HIP and PL. Figure S23. Cell type specific expression analysisof female biased genes in STR, TC and THA. Figure S24. Cell type specific expression analysisof male biased genes in CBC, CC, FC, HIP, MED and OC. Figure S25. Cell type specific expression analysisof male biased genes in PL, STR, TC and THA. Figure S26. Known motif enrichment analysis by HOMER in the promoters of the female-biased genes and male-biased genes. Figure S27.Schematic diagram of additional workflow to generate sex-biased gene list.The number of sex-biased genes from the additional workflow. Figure S28.The number of female-biased genes across brain regions using additional workflowThe number of male-biased genes across brain regions using additional workflow.The correlation heatmap of female-biased genes using additional workflow.The correlation heatmap of male-biased genes using additional workflow.The percentage of overlap between Androgen receptor elementgenes and sex-biased genes, brain expressed genes, and brain regionally elevated genes using additional workflow.The percentage of overlap between Estrogen receptor elementgenes and sex-biased genes. brain expressed genes and brain regionally elevated genes using additional workflow. Figure S29.Fraction of sex-biased genes found at least in 40 primates using additional workflow.Fraction of sex-biased genes found at least in 160 primates using additional workflow.Gene ontology enrichment analysis of female-biased genes for biological process using additional workflow.Gene ontology enrichment analysis of male-biased genes for biological process using additional workflow.Gene ontology enrichment analysis of female-biased genes for molecular function using additional workflow.Gene ontology enrichment analysis of male- biased genes for molecular function using additional workflow. Figure S30.Gene ontology enrichment analysis of female-biased genes for cellular composition using additional workflow.Gene ontology enrichment analysis of male-biased genes for molecular cellular composition using additional workflow.DisGeNetenrichment of female-biased genes using additional workflow.) DisGeNetenrichment of male- biased genes using additional workflow. Figure S31. Gene ontology analysis of output from DAVIDfor biological process.The top GO terms in female-biased genes in THA region with background genes of THA gene expression data.The top GO terms in male- biased genes in THA region with background genes of THA gene expression data.