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| * 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 |
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| * 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 * 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 Readings
Lectures
Introduction to R Programming
Affymetrix Microarray Analysis using R Programming
Gene-set Enrichment Analysis
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/16369572Computational analysis of microarray data.
Quackenbush J.
Nat Rev Genet. 2001 Jun;2(6):418-27.
http://www.ncbi.nlm.nih.gov/pubmed/11389458
- General Reviews
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/18202032Bioinformatics 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
- 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
- Reviews on Methods and Tools
Pathway Analysis and Visualization
Network Analysis and Visualization