GO Workshop - Biomics meeting, November 2010

Link to Lecture PDF - click here

Link to Hands-on session - click here

Links to various databases and programs

Selected GO annotation tools:

• Ontologizer 2.0: http://compbio.charite.de/index.php/ontologizer2.html
• DAVID: http://david.abcc.ncifcrf.gov/
• WebGestalt: http://bioinfo.vanderbilt.edu/webgestalt/
• Onto-Express: http://vortex.cs.wayne.edu/ontoexpress/

• Gene Ontology website (including Amigo): http://www.geneontology.org/
• GOA: http://www.ebi.ac.uk/GOA/

• Identifier Conversion Tools: http://bip.weizmann.ac.il/toolbox/seq_analysis/annotation.html

References

• Review of GO
  Use and misuse of the gene ontology annotations
  Rhee SY, Wood V, Dolinski K, Draghici S.
  Nat Rev Genet. 2008 Jul;9(7):509-15.

• Review of 68 gene enrichment tools
  Bioinformatics 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.

• The Topology-weighted and Topolgy-elim algorithms
  Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
  Alexa A, Rahnenfuhrer J, Lengauer T.
  Bioinformatics. 2006 Jul 1;22(13):1600-7.

• The Parent-Child algorithms
  Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis
  Grossmann S, Bauer S, Robinson PN, Vingron M.
  Bioinformatics. 2007 Nov 15;23(22):3024-31.

• Ontologizer paper
  Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration
  Bauer S, Grossmann S, Vingron M, Robinson PN.
  Bioinformatics. 2008 Jul 15;24(14):1650-1.

• DAVID paper (including step-by-step instructions)
  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
  Huang da W, Sherman BT, Lempicki RA.
  Nat Protoc. 2009;4(1):44-57.