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| * '''R Programming''' * [[http://cran.r-project.org/doc/manuals/R-intro.pdf|An Introduction to R]] * '''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 Links == * [[http://www.liacs.nl/~hoogeboo/mcb/nature_primer.html|Nature Biotechnology Primers in Computational Biology]] |
Pathway Analysis Readings
Lectures
Introduction to R Programming
Affymetrix Microarray Analysis using R Programming
Gene-set Enrichment Analysis
Readings
R Programming
Statistics
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/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
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/19816451Pathway 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