Sheila Colby from Ingenuity Systems discusses Ingenuity’s approach to microRNA research, and recent updates to IPA that benefit researchers working with microRNAs or who are attempting to find more efficient ways of microRNA target prioritization. The latest release of IPA includes microRNA related content from miRecords and the peer reviewed literature, in addition to existing content from TarBase and TargetScan.
by Sheila Colby, Ph.D., Senior Scientific Product Marketing Manager, IPA
“I’ve looked at microRNAs from both sides now, from up and down, from in and out, and still somehow, it’s microRNA illusions I recall, I really don’t know microRNAs at all….” Ever feel that way? In 1969 when Joni Mitchell first sang this song about life, microRNA was yet to be discovered. But even now, when it comes to understanding the complex roles these tiny hairpin-shaped molecules play in gene regulation, how they impact phenotypes, and apply this knowledge in medicine, we still have a long way to go. If you are looking for a new approach to microRNA research, please read on to learn about the powerful new tools available in IPA.
The way Ingenuity saw it in 2010, realizing the potential of microRNA knowledge in biomarker research and medicine would require substantial innovation to provide an easy way to perform the combined analysis of microRNA and mRNA expression data. Researchers would also need the ability to visualize the patterns of expression of mRNA-microRNA pairs and understand what they mean with respect to specific observed changes in phenotypes or biological processes. To that end, we charted a course to deliver a faster, more comprehensive, biology-centric approach to microRNA target prioritization to the research community.
We feel that we have achieved this goal. As of March 2011, microRNA researchers have a powerful, all-in-one application that leverages an impressive collection of microRNA content, which enables them to look at many important aspects of microRNA biology needed for microRNA target prioritization. Today, IPA is the only bioinformatics software to support end-to-end microRNA target prioritization workflows.
Researchers can now visualize high-confidence microRNA-mRNA interactions relevant to their microRNA and mRNA expression data within a wealth of relevant published findings about disease processes and pathways of interest. They can apply various biological filters to quickly identify and prioritize the most promising targets by repeatedly refining the pool of targets based on relevant biological and experimental criteria. They can learn more about their results using links in IPA to quickly access information about clinical trials, biomarkers, and published articles. Most importantly, using the visualization tools in IPA, researchers can look at their target of interest as they appear in biological pathways, processes, and networks to better understand how the microRNAs and their targets mediate disease biology.
In March, we added more than 622,000 microRNA findings to the Ingenuity® Knowledge Base. This included both experimentally validated interactions fromTarBase and predicted interactions from TargetScan. For our September 2010 release, we added 15,000 more experimentally validated findings —over 13,100 manually curated from publications by Ingenuity scientists, plus 2,600 from miRecords — bringing the total number of microRNA-related findings to 640,000, which makes IPA one of the world’s leading catalogs of experimentally validated and high-confidence microRNA interactions. It is combination of the microRNA Target Filter with this wealth of relevant microRNA-mRNA interaction content that makes this unique new approach so valuable in target prioritization.
Dr. Arupa Ganguly Ph.D., Professor of Genetics at the Hospital of the University of Pennsylvania, recently shared how these new capabilities are making a difference in her research: “IPA and its microRNA Target Filter have been very impactful for our research. We compared gene expression signatures of matched normal retinal tissue and retinoblastoma tumor tissue, and then used IPA for biological analysis of the data. Using microRNA and mRNA from same tumors, we applied the microRNA Target Filter in combination with the content in IPA. This approach helped us rapidly narrow in on key microRNAs we thought to be involved with tumor progression.”
We can’t wait to hear more of your stories. Let us know how IPA or the microRNA Target Filter has helped you by submitting your story to our new Points for Pathways program.
If you’d like to learn more about the new ways IPA can help you look at your microRNA research, we invite you to register for a scientific webinar, watch our recorded presentation from Molecular Medicine this year, or read our microRNA white paper. Or, just sign up for a free trial of IPA to try out our microRNA Target Filter yourself.
Click here to go to the Ingenuity.com home page.