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| * [[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 |
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| * General Reviews * Microarray data analysis: from disarray to consolidation and consensus.<<BR>> |
* __General Reviews__ * ''Microarray data analysis: from disarray to consolidation and consensus.''<<BR>> |
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| * Computational analysis of microarray data.<<BR>> | * ''Computational analysis of microarray data.''<<BR>> |
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| * Reviews on Methods and Tools * Gene-set approach for expression pattern analysis.<<BR>> |
* __Reviews on Methods and Tools__ * ''Gene-set approach for expression pattern analysis.''<<BR>> |
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| * Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.<<BR>> | * ''Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.''<<BR>> |
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| * Enrichment Visualization * Enrichment map: a network-based method for gene-set enrichment visualization and interpretation.<<BR>> |
* __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>> |
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| * '''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 |
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| * '''Network 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 Readings === * [[http://www.liacs.nl/~hoogeboo/mcb/nature_primer.html|Nature Biotechnology Primers in Computational Biology]] == Interesting Research Applications of Pathway Analysis == * ''A transcriptional signature and common gene networks link cancer with lipid metabolism and diverse human diseases.''<<BR>> Hirsch HA, Iliopoulos D, Joshi A, Zhang Y, Jaeger SA, Bulyk M, Tsichlis PN, Shirley Liu X, Struhl K.<<BR>> Cancer Cell. 2010 Apr 13;17(4):348-61.<<BR>> http://www.ncbi.nlm.nih.gov/pubmed/20385360 * ''Functional impact of global rare copy number variation in autism spectrum disorders.''<<BR>> Pinto D et al.<<BR>> Nature. 2010 Jul 15;466(7304):368-72. Epub 2010 Jun 9.<<BR>> http://www.ncbi.nlm.nih.gov/pubmed/20531469 |
Contents
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
Other Useful Readings
Interesting Research Applications of Pathway Analysis
A transcriptional signature and common gene networks link cancer with lipid metabolism and diverse human diseases.
Hirsch HA, Iliopoulos D, Joshi A, Zhang Y, Jaeger SA, Bulyk M, Tsichlis PN, Shirley Liu X, Struhl K.
Cancer Cell. 2010 Apr 13;17(4):348-61.
http://www.ncbi.nlm.nih.gov/pubmed/20385360Functional impact of global rare copy number variation in autism spectrum disorders.
Pinto D et al.
Nature. 2010 Jul 15;466(7304):368-72. Epub 2010 Jun 9.
http://www.ncbi.nlm.nih.gov/pubmed/20531469