Codes and files for the original research article "Sex Differences in Gene Regulatory Networks During Mid-Gestational Brain Development"
contains the 120 mid-gestational brain homogenate samples analyzed throughout this article data was obtained in the repository https://figshare.com/articles/Summary_statistics_for_expression_quantitative_trait_loci_in_the_developing_human_brain_and_their_enrichment_in_neuropsychiatric_disorders/6881825
contains the covariates associated to the samples, obtained during e-mail exchange with corresponding author
contains the preparation of the expression data input to build co-expression and regulatory networks
- checks for data stratification by covariate (sex, age, RIN and batch), filters low variable genes, discards outliers, corrects of batch effect
creates and analyzes CEMiTool co-expression modules
- builds the co-expression network, calculates class specific activity, runs enrichment of biological processes in each of the modules, integrates PPI data
Results for the three enrichment analysis are included
builds and analyzes gene regulatory networks
builds the networks integrating RNA counts, PPI and motif data
creates differential modules and extracts biological meaning of differences in interactions
- CONDOR: clusters PANDA network elements into modules
- ALPACA: compares community structure between two modules
- enrichment of modules in biological processes databases, extraction of transcription factors and genes that drive these differences, enrichment of modules into cell type, disorders and hormone targets databases