Many experimental designs end up producing lists of hits, usually based around genes or transcripts. Sometimes these lists are small enough that they can be examined individually, but often it is useful to do a more structured functional analysis to try to automatically determine any interesting biological themes which turn up in the lists.

This course looks at the various software packages, databases and statistical methods which may be of use in performing such an analysis. As well as being a practical guide to performing these types of analysis the course will also look at the types of artefacts and bias which can lead to false conclusions about functionality and will look at the appropriate ways to both run the analysis and present the results for publication.

Course Content

• Functional databases
• Statistical test for testing functional enrichment
• Common artefacts in functional analysis
• Presenting functional analysis in publications
• Motif detection tools
• Network analysis methods
• Commerical functional analysis tools

Course Material

• Introduction to Gene List analysis lecture (pptx)
• Introduction to Gene List analysis lecture (pdf)
• Gene List analysis practical (docx)
• Gene List analysis practical (pdf)
• Artefacts and Presenting Results lecture (pptx)
• Artefacts and Presenting Results lecture (pdf)
• Artefacts and Presenting Results Practical (docx)
• Artefacts and Presenting Results Practical (pdf)
• Motif Searching lecture (pptx)
• Motif Searching lecture (pdf)
• Motif Searching practical (docx)
• Motif Searching practical (pdf)
• Networks and Interactions lecture (pptx)
• Networks and Interactions lecture (pdf)
• Networks and Interactions practical (docx)
• Networks and Interactions practical (pdf)
• Commerical Tools lecture (pptx)
• Commerical Tools lecture (pdf)
• Data for all practicals (zip, 5MB)