Transcriptomic analysis of CNS TB

Avril WAlters requested KEGG pathway analysis for this project. Previously I sent them differential gene expression testing results as well as transcription module testing results.

Pathway analysis was conducted using Signaling Pathway Impact Analysis ( [[[https://www.researchgate.net/publication/235418844_SPIA_Signaling_Pathway_Impact_Analysis_SPIA_using_combined_evidence_of_pathway_over-representation_and_unusual_signaling_perturbations#fullTextFileContent]]] )

After careful assessment of the fairly comprehensive results provided by the collaborators (all done in R), which included differential expression testing between different cell types (microglia, astrocytes, neurons) and treatments (H37Rv, control, BCG) and funtional enrichment analysis, I noticed a batch effect in the data. I will therefore have to redo all analyses after batch correction using Combat.