#acl All:read DanieleMerico:write,delete,revert
= Pathway Analysis Readings =
== Lectures ==
 * '''Introduction to R Programming'''
   * [[attachment:MicroarrayAnalysis_Rprog_L1.ppt]]
   * [[attachment:MicroarrayAnalysis_Rprog_L2.ppt]]
   * [[attachment:MicroarrayAnalysis_Rprog_L3.ppt]]
 * '''Affymetrix Microarray Analysis using R Programming'''
   * [[attachment:MicroarrayAnalysis_Rprog_L4.ppt]]
   * [[attachment:MicroarrayAnalysis_Rprog_L5.ppt]]
 * '''Gene-set Enrichment Analysis'''
   * [[attachment:OBI_EnrPathwAnalysis.ppt]]
== Readings ==
 * '''R Programming'''
 * '''Microarray Analysis'''
   * __General Reviews__
     * ''Microarray data analysis: from disarray to consolidation and consensus.''<<BR>>
     Allison DB, Cui X, Page GP, Sabripour M.<<BR>>
     Nat Rev Genet. 2006 Jan;7(1):55-65. Review. Erratum in: Nat Rev Genet. 2006 May;7(5):406.<<BR>>
     http://www.ncbi.nlm.nih.gov/pubmed/16369572
     * ''Computational analysis of microarray data.''<<BR>>
     Quackenbush J.<<BR>>
     Nat Rev Genet. 2001 Jun;2(6):418-27. <<BR>>
     http://www.ncbi.nlm.nih.gov/pubmed/11389458
 * '''Gene-set Enrichment Analysis'''
   * __Reviews on Methods and Tools__
     * ''Gene-set approach for expression pattern analysis.''<<BR>>
     Nam D, Kim SY.<<BR>>
     Brief Bioinform. 2008 May;9(3):189-97.<<BR>>
     http://www.ncbi.nlm.nih.gov/pubmed/18202032
     * ''Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.''<<BR>>
     Huang da W, Sherman BT, Lempicki RA.<<BR>>
     Nucleic Acids Res. 2009 Jan;37(1):1-13.<<BR>>
     http://www.ncbi.nlm.nih.gov/pubmed/19033363
   * __GSEA__
     * ''Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.''<<BR>>
     Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP.<<BR>>
     Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50.<<BR>>
     http://www.ncbi.nlm.nih.gov/pubmed/16199517
   * __Enrichment Visualization__
     * ''Enrichment map: a network-based method for gene-set enrichment visualization and interpretation.''<<BR>>
     Merico D, Isserlin R, Stueker O, Emili A, Bader GD.<<BR>>
     PLoS One. 2010 Nov 15;5(11):e13984.<<BR>>
     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.''<<BR>>
     Cline MS et al.<<BR>>
     Nat Protoc. 2007;2(10):2366-82.<<BR>>
     http://www.ncbi.nlm.nih.gov/pubmed/17947979