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
    1. Matthew Whiteside/Notebook/Malaria Microarray/2009/02/09
  2. Read up on malaria pathogenesis. What are key genes, pathways?
    Entries
    1. Matthew Whiteside/Notebook/Malaria Microarray/2009/01/27
  3. Familiarize with bioconductor. How to load GEO datasets? How to perform meta-analysis?
    Entries
    1. Matthew Whiteside/Notebook/Malaria Microarray/2009/02/11
    2. Matthew Whiteside/Notebook/Malaria Microarray/2009/03/04
  4. Familiarize with public human malaria microarray datasets. Normalized? Platform?
    Entries
    1. Matthew Whiteside/Notebook/Malaria Microarray/2009/01/29
  5. Familiarize with meta-analysis & sysbio analysis tools
    Entries
    1. Matthew Whiteside/Notebook/Malaria Microarray/2009/02/10
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