February 21, 2019

New step-by-step protocol for common omics analyses fills 10-year gap in training resources

Juri Reimand

Expert group develops comprehensive guide for the interpretation and visualization of gene lists, replacing outdated, decade-old protocols

The importance of understanding biological pathways – or how our genes work together – is becoming increasingly evident, but pathway analysis remains a major challenge for many basic and biomedical researchers. Current computational tools can help simplify this analysis, but there is no established guide or standard for using these tools in practice.

To fill this gap, a team of experts from OICR and the Bader Lab at the University of Toronto recently published a comprehensive, step-by-step guide to pathway enrichment analysis that brings together their highly-recommended tools into one protocol. The complete protocol, which is now published in Nature Protocols, can be performed in less than five hours and can be used by researchers with no prior training in bioinformatics or computational biology.

“These days, almost every omics study needs to include pathway enrichment analysis, but it has been over a decade since a comprehensive protocol for these analyses has been published,” says Dr. Jüri Reimand, Principal Investigator at OICR and co-lead author of the protocol. “Our new methods are designed to guide researchers through their analyses and serve as a practical resource for their studies.”

Each step of the protocol is supported with detailed instructions and valuable troubleshooting information, which were designed in large part by Ruth Isserlin, co-lead author and Senior Bioinformatics Analyst in the Bader Lab.

Recently, the methods were used to identify a therapeutic target for ependymoma, a prevalent type of childhood brain cancer that is notoriously difficult to treat. The pathway analysis, as described in Nature, led to a better understanding of why most ependymoma treatments are not effective and revealed a new treatment option that could stop the progression of the disease.

“Future cancer research discoveries rely on our understanding of biological pathways,” says Reimand. “This protocol provides a resource from which we can build our understanding and explore previously uncharted relationships between our genes.”