Microarray analysis techniques: Difference between revisions

Revision as of 21:10, 16 October 2008

Revision as of 20:01, 31 October 2008

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Commercial systems for gene network analysis such as Ingenuity <ref> {{cite web |url=http://www.ingenuity.com/ |title=Ingenuity Systems |accessdate=2007-12-31 |format= |work=}} </ref> and Pathway studio<ref>{{cite web |url=http://www.ariadnegenomics.com/products/pathway-studio/ |title=Ariadne Genomics: Pathway Studio |accessdate=2007-12-31 |format= |work=}}</ref> create visual representations of differentially expressed genes based on current scientific literature. Non-commercial tools such as [[GenMAPP]] also aid in organizing and visualizing gene network data procured from one or several microarray experiments. A wide variety of microarray analysis tools are available through [[Bioconductor]] written in the [[R programming language]]. The frequently cited SAM Excel module and other microarray tools <ref>[{{cite web |url=http://www-stat.stanford.edu/~tibs/SAM/ |title=Significance Analysis of Microarrays |accessdate=2007-12-31 |format= |work=}}]</ref> are available through Stanford University. Another set is available from Harvard and MIT<ref>{{cite web |url=http://www.broad.mit.edu/tools/software.html |title=Software - Broad |accessdate=2007-12-31 |format= |work=}}</ref>.

Specialized software tools for statistical analysis to determine the extent of over- or under-expression of a gene in a microarray experiment relative to a reference state have also been developed to aid in identifying genes or gene sets associated with particular [[phenotype]]s. One such method of analysis, known as Gene Set Enrichment Analysis (GSEA), uses a [[Kolmogorov-Smirnov]]-style statistic to identify groups of genes that are regulated together <ref>{{cite journal |author=Subramanian A, Tamayo P, Mootha VK, ''et al'' |title=Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=102 |issue=43 |pages=15545–50 |year=2005 |pmid=16199517 |doi=10.1073/pnas.0506580102}}</ref>. This third-party statistics package offers the user information on the genes or gene sets of interest, including links to entries in databases such as NCBI's [[GenBank]] and curated databases such as Biocarta <ref>{{cite web |url=http://www.biocarta.com/ |title=BioCarta - Charting Pathways of Life |accessdate=2007-12-31 |format= |work=}}] </ref> and [[Gene Ontology]]. Related system, PAINT<ref>{{cite web |url=http://www.dbi.tju.edu/dbi/staticpages.php?page=tools&menu=37 |title=DBI Web |accessdate=2007-12-31 |format= |work=}}}</ref> and SCOPE <ref>{{cite web |url=http://genie.dartmouth.edu/scope/ |title=SCOPE |accessdate=2007-12-31 |format= |work=}}</ref>performs a statistical analysis on gene promoter regions, identifying over and under representation of previously identified [[transcription factor]] response elements. Another statistical analysis tool is Rank Sum Statistics for Gene Set Collections (RssGsc), which uses rank sum probability distribution functions to find gene sets that explain experimental data<ref>{{cite web |url=http://rssgsc.sourceforge.net/ |title=RssGsc |accessdate=2008-10-15 |format= |work=}}</ref>.

==References==