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