In this project, I will be performing a differential expression meta-analysis on Mice infected by WNV. Specifically, I will be looking for genes that are uniquely expressed upon infection by infective WNV but are common across different neuronal tissue types.

I will be including the following experiments from the Gene Expression Omnibus into my analysis: GSE78888, GSE77193, GSE68380, GSE77192, and GSE67473.

To do this, I will first perform DEA on all the experiments individually, comparing WNV infection to control condition for both WT and the deletion strain E218A (which attenuates WNV) at a single timepoint of 24 hrs post infection.

I will then perform meta analysis using MetaVolcanoR with included experiments for WT WNV infection and then perform a separate meta analysis with E218A WNV infection. I will compare the hit lists to identify genes specific to the infection response but not inflammation in neuronal tissue as well as one lymph node.

By performing a meta-analysis I hope to identify genes with strong evidence differential expression upon WNV infection brain-wide.

├── BIOL-430.Rproj ├── Figures │ ├── Heatmap.png # Heatmap of sample-sample correlations │ ├── PCA.png # Principal Component Analysis of samples │ ├── VennDiagram.png # Overlap of DEGs between tissue types │ └── VolcanoPlot.png # Volcano plots of WT and #E218A DEGs ├── Outputs │ ├── E218A_GO_Terms.csv # Gene Ontology terms for just E218A strain WNV │ ├── Shared_GO_Terms.csv # Gene Ontology terms shared between strains │ └── WT_GO_Terms.csv # Gene Ontology terms for just WT WNV ├── README.md └── Scripts ├── Analysis.R # Script containing all analyses └── Install_Packages.R # Script to install dependencies