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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 * __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 |
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| * __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 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
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
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