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The Ingenuity Scientific Seminar series explores in detail how Ingenuity product solutions can be used to answer specific scientific questions. Click on a topic title below to view a past Scientific Seminar video. |
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Past Scientific Seminar Videos
Gene Expression Analysis Using Ingenuity iReport to Analyze Response to H1N1 Influenza[video runtime: 49:58 minutes]
Presented by Jamie L. Fornak, Ph.D. MPH
This webinar uses previously published data from an influenza study to demonstrate the ability of Ingenuity® iReport™ to correctly identify expected results and gain additional novel biological insights from gene expression data. Lee et al. originally performed gene expression analysis on human type-I like alveolar epithelial cells that were mock infected or infected with seasonal H1N1or pandemic H1N1. Two separate iReport analyses were generated from this dataset: one comparing mock infection to seasonal H1N1 infection and another comparing mock infection to pandemic H1N1 infection. See how iReport expanded the insights described in the original publication and provided additional genes of interest for potential follow up studies in the areas of transcription and mRNA transport.
IPA and Coronary Artery Disease: A Case Study from Harvard[video runtime: 36:23 minutes]
Presented by Dr. Jochen Danny Muehlschlegel, M.D., Harvard Medical School
See how IPA was used for the discovery of novel pathways of affected genes in coronary artery disease. Cardiopulmonary bypass (CPB) with cardioplegic arrest is associated with ischemia leading to metabolic substrate depletion, reperfusion injury, apoptosis and necrosis. The study hypothesized that human left ventricular (LV) myocardium responds differently to the stress of (CPB) depending on the presence or absence of coronary artery disease (CAD). Therefore, they assessed differences in gene expression in patients undergoing aortic valve replacement (AVR) with (CPB) prior to and after cardioplegic arrest using whole-genome transcriptional profiling.
A Combined Biological and Bioinformatic Analysis of Primary and Metastatic Tissues from NGS Ewing's Sarcoma Patients[video runtime: 58:00 minutes]
Presented by Jean-Noel Billaud, Ph.D., Ingenuity Systems and Sylvain Foissac, Ph.D., Integromics
The Ewing's Sarcoma family of tumors is a category of cancers that predominantly affects teenagers between the ages of 10 to 20. Learn how Ingenuity Systems' IPA software and Integromics' SeqSolve software were used to investigate Ewing's Sarcoma patient samples generated from Helicos' NGS technology. We will present a combined bioinformatic and biological analysis of Ewing's Sarcoma patient samples, focusing on the differences between primary and metastatic tissues. IPA was used to analyze the significantly regulated genes and Integromics' NGS SeqSolve software was used to prepare the RNA-Seq data. IPA's new transcription factor analysis tool and downstream effects map were used to help narrow down targets and visualize the biological networks.
Using IPA to Analyze Illumina RNA-Seq Data Reveals Abundance-Specific Biological Signatures in Alzheimer's Disease [video runtime: 33:44 minutes]
Presented by Darryl Gietzen, Ph.D., Ingenuity Systems
IPA was used to interpret Alzheimer's disease biology by comparing Illumina RNA-Seq data from Alzheimer's disease (AD) and normal brain samples. This analysis revealed very specific biological changes in certain classes of transcript expression, demonstrating how the unique benefits of RNA-Seq can help characterize disease changes. See how IPA maximizes RNA-Seq data analysis, how grouping and analyzing all significantly changed genes in RNA-Seq data can provide pathway level information, and how the sensitivity and accuracy of RNA-Seq enables pathway analysis on a subset of genes to elucidate more subtle biological changes.
Utilizing IPA for the Discovery and Development of New Pain Therapeutics [video runtime: 18:29 minutes]
Presented by Meredith Prysak, Ph.D., Aestus Therapeutics
Learn how Dr. Prysak utilized IPA to investigate the neuropathic pathways related to pain. In the United States, more than 39 million people suffer from neuropathic pain related to postherpetic neuralgia, trigeminal neuralgia, AIDS-related neuropathy, diabetic neuropathy, chronic low back pain, and cancer neuropathy. Unfortunately, neuropathic pain is often intractable and resistant to available drug therapies, none of which achieve clinical significance greater than 50%. To address this problem of great clinical need and poor therapeutic response, new mechanisms of action must be identified for future pain therapeutics. Aestus Therapeutics has undertaken a project to identify novel biological pathways involved in neuropathic pain using genome-wide expression data from a variety of sources and models. IPA (as well as other bioinformatics tools) helped Aestus identify SEVEN novel biological pathways previously not associated with neuropathic pain. These SEVEN novel pathways are being targeted for novel pain therapies. These potential therapeutics have been pre-clinically tested in animal models, validating both the pathways and the targets. The lead compound for the project, ATx08-001, was recently advanced into the clinic by Aestus, and is currently in a Phase 2 trial for the treatment of post-herpetic neuralgia. In this presentation, you will see how IPA was used to filter and explore existing data to investigate affected pathways and ultimately pathways for novel neuropathic pain therapies for patients.
NGS: Insights Into Prostate Cancer Mechanisms Via Integrated In Silico RNA-Seq Analysis of NGS Patient Data [video runtime: 14:07 minutes]
Presented by Sandeep Sanga, Ph.D., Ingenuity Systems
The goal of this study was to get novel insights into the mechanisms of disease by leveraging the rapidly growing next generation sequencing (NGS) data, and in particular, human transcriptome data through in silico data analysis and interpretation using Ingenuity IPA and CLC bio. The analysis of altered expression of genes and regulatory regions can pinpoint specific pathways and processes activated in growing cancer cells within tumors. IPA helped determine these activated pathways and networks and shed light on dysregulated processes, informed treatment options and highlighted potential biomarkers to further the ultimate goal to improve patient prognosis and treatment.
Biomarkers for Prostate Cancer: How IPA Can Help Explore Potential Biomarkers for a Complex Disease [video runtime: 39:31 minutes]
Presented by Jean-Noel Billaud, Ph.D., Ingenuity Systems
Learn how Dr. Billaud uses IPA to achieve novel insights into the mechanisms of prostate cancer by utilizing IPA networks, gene views and canonical pathways. Dr. Billaud utilized the IPA biomarker filter, reagent view, function & disease overlay, and SNP data to identify the clinical aspects of prostate cancer.
MicroRNA: Using IPA's microRNA Target Filter to Identify and Prioritize microRNA Targets for Melanoma [video runtime: 25:13 minutes]
Presented by Karen Lavery, Ph.D., Ingenuity Systems
Learn how IPA's microRNA Target Filter is used to identify high priority targets in a metastatic melanoma data set. The IPA microRNA Target Filter was able to narrow down the three most relevant targets from 13,000 potential microRNA targets. Melanoma targets were analyzed in IPA's cancer disease pathways, cell growth signaling pathways, and networks. In 2011, the microRNA Target Filter was added into IPA, as well as rich microRNA content. IPA has the only commercially-available microRNA Target Filter. IPA's microRNA content derives from TargetScan, TarBase, miRecords and Ingenuity Expert Findings (manually curated literature added into the Ingenuity Knowledge Base).
Using IPA to Explore Pathways and Investigate Effects of Insulin Resistance on Human Adipose [video runtime: 23:19 minutes]
Presented by Shelley des Etages, Ph.D., Pace University, formerly Pfizer
See how to use IPA to investigate metabolic and signaling pathways affected by the insulin resistant state for the baseline adipose samples. Insulin resistance is a key component of Type II Diabetes. Essentially, it reflects the state in which peripheral tissues such as liver, muscle and adipose become less responsive to insulin. The increased insulin output required to maintain glucose homeostasis eventually leads to loss of pancreatic islet function and frank diabetes. Sears et al published a study examining adipose and muscle samples extracted from insulin sensitive and resistant subjects at baseline, and then 3 months after thiazolidinedione treatment. In this presentation, you will see how IPA was used to filter and explore existing data to investigate affected pathways and ultimately identify a transcription factor that may serve as a link between TLR2 signaling and adiponectin levels.
Biomarkers and microRNA: Integrative Analysis of microRNA and mRNA as Biomarkers for Ovarian Cancer [video runtime: 11:11 minutes]
Presented by Stuart Tugendreich, Ph.D., Ingenuity Systems
See how IPA was used to identify microRNA biomarkers of ovarian cancer and explore their mRNA targets and possible roles in disease. IPA helped identify networks of microRNAs and their predicted targets, as well as the implicated pathways and cellular types affected by more aggressive tumors. You'll learn about the microRNA Target Filter, a powerful component of IPA that allows for the rapid identification and prioritization of microRNA Targets based upon unique filtering tools and content taken from TargetScan and TarBase, as well as the comprehensive biomarker content and capabilities within IPA.
A Systems Toxicology Approach To Understanding Drug Toxicity And Compound Prioritization [video runtime: 36:18 minutes]
Presented by Kevin T. Morgan, Old Dogs in Training, LLC and Ke Xu, Department of Pharmacology, UNC Chapel Hill
Sound decisions require sound knowledge. Whilst drowning in a swelling sea of information, we are given little time for the reflective contemplation needed to derive knowledge from this information. Epistemology, which concerns itself with the origins and nature of knowledge, indicates that the nature of knowledge itself is influenced by our information-generating technologies (Postman N, 1986, "Amusing Ourselves To Death"). Once again, we are feeling the impact of new technologies on the process of knowledge generation in the form 'omics' information overload! For instance, Transcriptomics requires the interpretation of large-scale transcriptional responses to a range of physiological variables, including toxic chemicals (Toxicogenomics). Both Transcriptomics and Toxicogenomics, which have been used for decades, are contributing to information overload at an accelerating rate. The interpretation of large-scale gene expression data requires a broad general understanding of biological systems, a feel for the dynamics of networks and their embedded pathways, plus the availability of appropriate analytical software and time to think without interruption. Unfortunately, in spite of a massive investment in omics technologies (hardware and software), most Toxicogenomic studies receive inadequate interpretation due to (a) insufficient training of staff (wetware) in transcriptome physiology and pathophysiology, and (b) inadequate allocation of trained wetware resources to the task. The need for structured education in this field will be discussed in relation to Bioenergetics, Dynamics, and type II diabetes drug targets, through the application of Array Studio and IPA® software to publicly available datasets.
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