Pathway Analysis Readings

Lectures

Introduction to R Programming
Affymetrix Microarray Analysis using R Programming
- MicroarrayAnalysis_Rprog_L4.ppt
- MicroarrayAnalysis_Rprog_L5.ppt
Gene-set Enrichment Analysis
- OBI_EnrPathwAnalysis.ppt

Readings

R Programming
Microarray Analysis
- General Reviews
  - Microarray data analysis: from disarray to consolidation and consensus.
    Allison DB, Cui X, Page GP, Sabripour M.
    Nat Rev Genet. 2006 Jan;7(1):55-65. Review. Erratum in: Nat Rev Genet. 2006 May;7(5):406.
    http://www.ncbi.nlm.nih.gov/pubmed/16369572
  - Computational analysis of microarray data.
    Quackenbush J.
    Nat Rev Genet. 2001 Jun;2(6):418-27.
    http://www.ncbi.nlm.nih.gov/pubmed/11389458
Gene-set Enrichment Analysis
- Reviews on Methods and Tools
  - Gene-set approach for expression pattern analysis.
    Nam D, Kim SY.
    Brief Bioinform. 2008 May;9(3):189-97.
    http://www.ncbi.nlm.nih.gov/pubmed/18202032
  - Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.
    Huang da W, Sherman BT, Lempicki RA.
    Nucleic Acids Res. 2009 Jan;37(1):1-13.
    http://www.ncbi.nlm.nih.gov/pubmed/19033363
- GSEA
  - Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
    Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP.
    Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50.
    http://www.ncbi.nlm.nih.gov/pubmed/16199517
- Enrichment Visualization
  - Enrichment map: a network-based method for gene-set enrichment visualization and interpretation.
    Merico D, Isserlin R, Stueker O, Emili A, Bader GD.
    PLoS One. 2010 Nov 15;5(11):e13984.
    http://www.ncbi.nlm.nih.gov/pubmed/21085593
Pathway Analysis and Visualization
Network Analysis and Visualization
- Cytoscape
  - Integration of biological networks and gene expression data using Cytoscape.
    Cline MS et al.
    Nat Protoc. 2007;2(10):2366-82.
    http://www.ncbi.nlm.nih.gov/pubmed/17947979