mouse-gut-brain

Repository for the analysis of primate GM effects on mouse brain gene expression

This repository contains scripts used in our analysis of primate GM effects on mouse brain gene expression.

We ran most analysis steps using R (v4.1). We recommend the following utility or visualization packages to extend base R's functionality.

Inputs

The following files are expected:

Mouse experiment - brain RNAseq data:

• A .csv file containing count data data/counts.csv
• A .csv file containing metadata data data/mouse_meta.csv
• A .csv file containing technical metadata data data/mouse_tech_meta.csv
• A .csv file containing normalized expression data data/exp-data-matched-to-pathways.csv

Mouse experiment - GM data:

• A .csv file containing pathway data data/pathway-data-matched-to-expression.csv

Published datasets:

• An .rds file containing primate expression data (from Zhu et al. 2018) data/human_v_macaque_zhu_MFC.rds
• A .csv file containing the results from Dumas et al. 2021 data/dumas.csv
• A .tsv file containing disease risk genes from the DISEASES database data/human_disease_associations.tsv
• A .txt file containing network parameters for MiMeNet analysis data/network_parameters.txt

Pipeline

• Key libraries: variancePartition, BRETIGEA, biomaRt, ggplot2, corrplot

scripts/mouse-code-final.R

MiMeNet analysis

• Key libraries: MiMeNet_train.py

scripts/microbiome.sh