Gene set analysis



This section collects together tools that can be used in gene set analysis. 

PROGRAMS AVAILABLE

• DAVID
• GSZ
• GoMiner
• GOstat
• Onto-express
• GoToolBox
• FatiGO
• GFINDer
• GOBar
• GSEA
• Ontologizer (contains MGSA method) 



Quite large list of similar tools can be found from the file

http://www.nature.com/nprot/journal/v4/n1/extref/nprot.2008.211-S1.xls

DESCRIPTION OF PROGRAMS

DAVID

DAVID (the database for annotation, visualization and integrated discovery) consist of integrated biological knowledge base and analytic tools aimed at systematically extract biological meaning from large gene/protein lists. As input it takes a gene list. Some of the analysis in web based version can be run with very large gene lists but some of the analysis are restricted to 3000 genes list. 

website: DAVID

Download:

Reference: Huang et al.Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources.doi:10.1038/nprot.2008.211

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GSZ

GSZ is  meant for robust extraction of functional signals from gene set analysis. It uses generalized threshold free scoring function. 

website: GSZ

Download: GSZ-matlab package 

Reference: Törönen et al. Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function. doi:10.1186/1471-2105-10-307

Ontologizer 

Ontologizer is a free and open-source software  (Java application) that implements a large number of GO enrichment methods and enables visualization of the results. Among these tools is implemented method called MGSA (model-based gene set analysis).  

website: Ontologizer

Reference: Bauer et al. GOing Bayesian: model-based gene set analysis of genome-scale data. doi:10.1093/nar/gkq045

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USEFUL DATABASES

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REVIEW ARTICLES

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OTHER ARTICLES

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USEFUL LINKS

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