Commercial tools for gene list analysis

Boo VirkBoo.virk@babraham.ac.uk

v1.0

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

Commercial tools for gene list analysis

• Many available – examples include:

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

Commercial tools for gene list analysis

• Many available – examples include:

Ingenuity Pathway Analyser(IPA®)

Top Pathways

Function Heatmap

Identify potential upstream regulators

Networks

Summary Report

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

• 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

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