#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.<
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Allison DB, Cui X, Page GP, Sabripour M.<
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Nat Rev Genet. 2006 Jan;7(1):55-65. Review. Erratum in: Nat Rev Genet. 2006 May;7(5):406.<
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http://www.ncbi.nlm.nih.gov/pubmed/16369572
* Computational analysis of microarray data.<
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Quackenbush J.<
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Nat Rev Genet. 2001 Jun;2(6):418-27. <
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http://www.ncbi.nlm.nih.gov/pubmed/11389458
* '''Gene-set Enrichment Analysis'''
* Reviews on Methods and Tools
* Gene-set approach for expression pattern analysis.<
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Nam D, Kim SY.<
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Brief Bioinform. 2008 May;9(3):189-97.<
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http://www.ncbi.nlm.nih.gov/pubmed/18202032
* Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.<
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Huang da W, Sherman BT, Lempicki RA.<
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Nucleic Acids Res. 2009 Jan;37(1):1-13.<
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http://www.ncbi.nlm.nih.gov/pubmed/19033363
* Enrichment Visualization
* Enrichment map: a network-based method for gene-set enrichment visualization and interpretation.<
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Merico D, Isserlin R, Stueker O, Emili A, Bader GD.<
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PLoS One. 2010 Nov 15;5(11):e13984.<
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http://www.ncbi.nlm.nih.gov/pubmed/21085593
* '''Pathway Analysis and Visualization'''
* '''Network Analysis and Visualization'''