Pathway Analysis Readings

Lectures

• Introduction to R Programming

  • MicroarrayAnalysis_Rprog_L1.ppt

  • MicroarrayAnalysis_Rprog_L2.ppt

  • MicroarrayAnalysis_Rprog_L3.ppt

• Affymetrix Microarray Analysis using R Programming

  • MicroarrayAnalysis_Rprog_L4.ppt

  • MicroarrayAnalysis_Rprog_L5.ppt

• Gene-set Enrichment Analysis

  • OBI_EnrPathwAnalysis.ppt

Readings

• R Programming

  • An Introduction to R

• Statistics

  • Online statistical reference by Statsoft

• Primers on Useful Data Analysis Techniques

  • Principal Component Analysis

    • What is principal component analysis?
      Ringnér M.
      Nat Biotechnol. 2008 Mar;26(3):303-4.
      http://www.ncbi.nlm.nih.gov/pubmed/18327243

  • Clustering

    • How does gene expression clustering work?
      D'haeseleer P.
      Nat Biotechnol. 2005 Dec;23(12):1499-501.
      http://www.ncbi.nlm.nih.gov/pubmed/16333293

  • Multiple Testing Correction

    • How does multiple testing correction work?
      Noble WS.
      Nat Biotechnol. 2009 Dec;27(12):1135-7.
      http://www.ncbi.nlm.nih.gov/pubmed/20010596

• 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

• Network Analysis and Visualization

  • General Reviews

    • How to visually interpret biological data using networks.
      Merico D, Gfeller D, Bader GD.
      Nat Biotechnol. 2009 Oct;27(10):921-4.
      http://www.ncbi.nlm.nih.gov/pubmed/19816451

    • Pathway information for systems biology.
      Cary MP, Bader GD, Sander C.
      FEBS Lett. 2005 Mar 21;579(8):1815-20.
      http://www.ncbi.nlm.nih.gov/pubmed/15763557

  • 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

• Pathway Analysis and Visualization

  • Methods

    • A novel signaling pathway impact analysis.
      Tarca AL, Draghici S, Khatri P, Hassan SS, Mittal P, Kim JS, Kim CJ, Kusanovic JP, Romero R.
      Bioinformatics. 2009 Jan 1;25(1):75-82.
      http://www.ncbi.nlm.nih.gov/pubmed/18990722

Other Useful Links

• Nature Biotechnology Primers in Computational Biology