1. Commercial tools for gene list analysis Boo Virk Boo.virk@babraham.ac.uk v1.0

2. Why use commercial tools? Benefits: Each tool has their own large database Databases are updated regularly and curated All analysis can be done in one package Overlay different projects/experiments to see potential links Customer Support

3. Commercial tools for gene list analysis Many available – examples include:

4. Advaita - Only pay for reports you will publish Thomson Reuters – more focussed on human diseases and drug discovery Agilent Technologies – integrated with Ingenuity Pathway Analysis (IPA) and Metacore

5. Commercial tools for gene list analysis Many available – examples include:

6. Ingenuity Pathway Analyser (IPA®)

7. Top Pathways

8. Function Heatmap

9. Identify potential upstream regulators

10. Networks

11. Summary Report NOTE: IPA uses Fisher’s Exact test right tailed test – which is twice as likely to reach significance!

12. Analysis is no different from free tools Statistics and outputs are similar to those obtained from free web based resources £££££ Are larger databases necessarily better? Limitations of Commercial tools

13. Which tool to use? There are different types of software available, both free and commercial Try a few, and find the tool that’s best for your experiments and needs Using more than one tool to analyze your data may provide new insights or lend extra confidence to your results