User:Matthew Whiteside/Notebook/Malaria Microarray/Tasks/Task3
TASK3: Human Meta-analysis of Malaria microarray data
- combine publicly available human datasets in meta-analysis
- identify common pathways, hubs, DE genes associated with all types of malaria
- determine key human pathways involved in malaria infection. Are they similar/different than murine infection model.
Analysis to consider:
- Develop statistical test for hub
- Use Dr. Ester's subnetwork clustering tool (cluster based on connectivity and DE)
- Transciption factor ORA
- Redo Pathway & GO term ORA - using InnateDB
To Do List
- Read up on microarray meta-analysis. How to combine platforms, studies etc.
- Read up on malaria pathogenesis. What are key genes, pathways?
- Familiarize with bioconductor. How to load GEO datasets? How to perform meta-analysis?
- Familiarize with public human malaria microarray datasets. Normalized? Platform?
- Familiarize with meta-analysis & sysbio analysis tools