User:Matthew Whiteside/Notebook/Malaria Microarray/Tasks/Task3

TASK3: Human Meta-analysis of Malaria microarray data

Notes

Goals:

• 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

1. Read up on microarray meta-analysis. How to combine platforms, studies etc.

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2. Read up on malaria pathogenesis. What are key genes, pathways?

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3. Familiarize with bioconductor. How to load GEO datasets? How to perform meta-analysis?

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4. Familiarize with public human malaria microarray datasets. Normalized? Platform?

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5. Familiarize with meta-analysis & sysbio analysis tools

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