Training for IPA 9.0

Ingenuity is offering training around the new features in IPA 9.0.   Visit the IPA Training page for more details.

What’s New in IPA 9.0

This webinar will demonstrate the new features being released into IPA 9.0. The new, one-of-a-kind microRNA Target Filter combined with newly added microRNA content (from TarBase and TargetScan) provides insight into the biological effects of microRNAs. You’ll see how you can explore microRNA-mRNA pairings and then easily filter lists of microRNA targets based on relevant biological characteristics, such as association with disease, pathways, cell lines, tissues, molecular types, species, and more. You’ll also learn about new support for RNA-Seq data in IPA and integrations with upstream NGS partners. Lastly, you’ll get an overview of usability and design enhancements to IPA that help you quickly access important parts of IPA, plus a new Customer Support Portal.

Thursday, March 17, 2011

Using IPA 9.0 to explore microRNA impacts on molecular mechanisms of disease

Wednesday, March 16, 2011

IPA 9.0 addresses the critical need to identify and prioritize microRNA targets using biology by providing a microRNA Target Filter. In this seminar, we demonstrate the use of IPA to identify high priority targets of interest in a metastatic melanoma data set. Over 13,000 potential microRNA targets were focused to ˜300 using melanoma-relevant biology such as cancer disease pathways or cell growth signaling pathways. The target list was refined to ˜30 targets using a metastatic melanoma mRNA gene expression data set. Since many microRNAs effectively down-regulate target mRNA levels, results were limited to microRNA-target pairs with opposite expression patterns. The IPA microRNA Target Filter identified three targets with importance to melanoma and metastasis: ITGB1, KIT, and MC1R. Pathway tools in IPA lead to the discovery that both KIT and MC1R receptors control Melanocyte Development and Pigmentation Signaling. Both genes have additional supporting references for a role in metastasis and melanoma and are good targets for further investigation.

Oral Squamous Cell Carcinoma RNA-Seq Analysis: Using IPA to Understand Variants

Wednesday, March 23, 2011

In this case study, RNA-Seq data from oral squamous cell carcinoma (OSCC) were analyzed using IPA 9.0 to identify candidate biomarkers and gain understanding of the biology of OSCC. Results identified six variants that were up-regulated in OSCC for all patients, including SERPIN and LAMC-2. These genes also were in studies as biomarkers for this disease. Analysis of up-regulated genes showed an impact on cell cycle, including changes in expression of Cell Cycle G2/M Checkpoint Signaling genes for all 3 patients. One goal of the RNA-Seq method is to examine commonalities and differences for transcripts in a set of patients. In the OSCC samples, cell cycle clearly was affected, and up-regulation was consistent for CDC2 (CDK1) and MYT1, however the specific signatures varied for p53 and others upstream in the pathway. Down-regulated pathways included Complement Signaling and Calcium Signaling. In the Calcium pathway, expression of SERCA (ATP2A), sarcoplasmic reticulum receptors, actins, and troponins was decreased in OSCC, suggesting an effect on cell growth as controlled by this pathway. Combined together, RNA-seq data and IPA analysis revealed target areas for additional research, while also retaining the granularity of original transcript variants from the original data.

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