README.md

Codes and files for the original research article "Sex Differences in Gene Regulatory Networks During Mid-Gestational Brain Development"

Data folders:

raw data:

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

metadata:

contains the covariates associated to the samples, obtained during e-mail exchange with corresponding author

Analysis:

0. Preprocessing:

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

1. CEMiTool:

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

2. netZoo:

builds and analyzes gene regulatory networks

2.1. PANDA

builds the networks integrating RNA counts, PPI and motif data

2.2. CONDOR + ALPACA

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