pituitary-LPS-gene-analyses

This repository details gene expression analyses from Castro-Garcia, Velez et al. 2023

Analyses are broken into two parts:

1. Module detection, differential expression and integration of LPS-induced genes in mouse pituitary: WGCNA and DE from LPS induction.R

2. Integration of LPS DEGs with GTEx dataset: GTEx integration of LPS DEGs.R

Datasets used in this study are available here:

1. Filtered GTEx gene expression data (V8) to compare genetic correlation structure of genes across tissues: GTEx NA included env

Source: https://elifesciences.org/articles/76887 and https://gtexportal.org/home/

2. GTEx subject annotations including reported sex: GTEx_Analysis_v8_Annotations_SubjectPhenotypesDS.txt

Source: https://elifesciences.org/articles/76887 and https://gtexportal.org/home/

3. List of all known secreted proteins supplied by UniProt: human secreted proteins.tab

Source: https://www.uniprot.org/ and https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5935137/

4. All Normalize gene expression counts, metadata and info for LPS-induced gene expression via RNA-Seq: 20201006_lawson_nicholas_....csv

Source: This study