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

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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.
    Entries
  2. Read up on malaria pathogenesis. What are key genes, pathways?
    Entries
  3. Familiarize with bioconductor. How to load GEO datasets? How to perform meta-analysis?
    Entries
  4. Familiarize with public human malaria microarray datasets. Normalized? Platform?
    Entries
  5. Familiarize with meta-analysis & sysbio analysis tools
    Entries