Thy1-haSyn and WT RNA-seq WGCNA - Brain-UPR (red) module

Gene expression profiling was performed on gut (colon) and brain (striatal) tissue from mice overexpressing human wild type α–synuclein (Thy1-haSyn) and wild-type (WT) mice aged 1 and 3 months using 3′ RNA sequencing. Weighted gene co-expression network analysis (WGCNA) was performed in R. Genes on the X chromosome, which contains the transgene, were excluded. For colon samples, a signed network was constructed based on biweight midcorrelations with a soft power threshold of eight. The percent of outliers for biweight midcorrelations was restricted to 5%. Module detection used a cut height of 0.995, a minimum module size of 60, and a deep split level of 1. Highly correlated modules (>0.75) were merged. Analysis for striatum used the same parameters except for a soft threshold power of 12 and restriction of outliers for biweight midcorrelations to 1%.

This network contains selected nodes with module membership ≥ 0.6. Edge weights were derived from the adjacency matrix.


Full networks:
Colon: Thy1-haSyn and WT Colon RNA-seq WGCNA (d72dcf6e-eb40-11eb-b666-0ac135e8bacf) (ndexbio.org)

Brain: Thy1-haSyn and WT Striatum RNA-seq WGCNA (a207e9d0-5233-11ec-b3be-0ac135e8bacf) (ndexbio.org)

Consensus networks

Colon adjacency: Thy1-haSyn and WT RNA-seq WGCNA - Brain and colon consensus network (colon adjacency) (e87d7969-eb45-11eb-b666-0ac135e8bacf) (ndexbio.org)

Striatum adjacency: Thy1-haSyn and WT RNA-seq WGCNA - Brain and colon consensus network (brain adjacency) (d01c04e6-eb45-11eb-b666-0ac135e8bacf) (ndexbio.org)

Code is available at https://github.com/videlock/Thy1-haSyn-Gut-Brain