#acl All:read DanieleMerico:write,delete,revert

<<TableOfContents(3)>> 

= 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'''
   * [[http://cran.r-project.org/doc/manuals/R-intro.pdf|An Introduction to R]]
   * [[http://cran.r-project.org/doc/contrib/Short-refcard.pdf|R Command Reference Card]]
 * '''Statistics'''
   * [[http://www.statsoft.com/textbook/|Online statistical reference by Statsoft]]
 * '''Primers on Useful Data Analysis Techniques'''
   * __Principal Component Analysis__
     * What is principal component analysis?<<BR>>
     Ringnér M.<<BR>>
     Nat Biotechnol. 2008 Mar;26(3):303-4.<<BR>>
     http://www.ncbi.nlm.nih.gov/pubmed/18327243
   * __Clustering__
     * How does gene expression clustering work?<<BR>>
     D'haeseleer P.<<BR>>
     Nat Biotechnol. 2005 Dec;23(12):1499-501.<<BR>>
     http://www.ncbi.nlm.nih.gov/pubmed/16333293
   * __Multiple Testing Correction__
     * ''How does multiple testing correction work?''<<BR>>
     Noble WS.<<BR>>
     Nat Biotechnol. 2009 Dec;27(12):1135-7.<<BR>>
     http://www.ncbi.nlm.nih.gov/pubmed/20010596
 * '''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
 * '''Network Analysis and Visualization'''
   * __General Reviews__
     * How to visually interpret biological data using networks.<<BR>>
     Merico D, Gfeller D, Bader GD.<<BR>>
     Nat Biotechnol. 2009 Oct;27(10):921-4.<<BR>>
     http://www.ncbi.nlm.nih.gov/pubmed/19816451
     * ''Pathway information for systems biology.''<<BR>>
     Cary MP, Bader GD, Sander C.<<BR>>
     FEBS Lett. 2005 Mar 21;579(8):1815-20.<<BR>>
     http://www.ncbi.nlm.nih.gov/pubmed/15763557
   * __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
 * '''Pathway Analysis and Visualization'''
   * __Methods__
     * A novel signaling pathway impact analysis.<<BR>>
     Tarca AL, Draghici S, Khatri P, Hassan SS, Mittal P, Kim JS, Kim CJ, Kusanovic JP, Romero R.<<BR>>
     Bioinformatics. 2009 Jan 1;25(1):75-82.<<BR>>
     http://www.ncbi.nlm.nih.gov/pubmed/18990722
=== Other Useful Readings ===
 * [[http://www.liacs.nl/~hoogeboo/mcb/nature_primer.html|Nature Biotechnology Primers in Computational Biology]]
== Interesting Research Applications of Pathway Analysis ==
 * ''A transcriptional signature and common gene networks link cancer with lipid metabolism and diverse human diseases.''<<BR>>
 Hirsch HA, Iliopoulos D, Joshi A, Zhang Y, Jaeger SA, Bulyk M, Tsichlis PN, Shirley Liu X, Struhl K.<<BR>>
 Cancer Cell. 2010 Apr 13;17(4):348-61.<<BR>>
 http://www.ncbi.nlm.nih.gov/pubmed/20385360
 * ''Functional impact of global rare copy number variation in autism spectrum disorders.''<<BR>>
 Pinto D et al.<<BR>>
 Nature. 2010 Jul 15;466(7304):368-72. Epub 2010 Jun 9.<<BR>>
 http://www.ncbi.nlm.nih.gov/pubmed/20531469