2013 IPA Fall Release Product Introduction Webinar [34:11 minutes]
Presented by Dr. Stuart Tugendreich, Scientific Director, IPA
See the whole picture! Powerful functionality enables you to understand causal connections between molecules and diseases. This Fall 2103 release of IPA® from Ingenuity® Systems has exciting new capabilities which enable interactive visual exploration of causality between molecules and disease, functions, or phenotypes.
Life Long Changes in DNA Methylation & ncRNAs in Fetal Alcohol Syndrome (FAS) [54:54 minutes]
Presented By: Ben Laufer, PhD Candidate, Western University, Ontario, Canada
Fetal alcohol spectrum disorders (FASDs) are characterized by life-long changes in gene expression, neurodevelopment and behavior. What mechanisms initiate and maintain these changes are not known, but current research suggests a role for alcohol-induced epigenetic changes. We assessed alterations to adult mouse brain tissue by assaying DNA cytosine methylation and small noncoding RNA (ncRNA) expression, specifically the microRNA (miRNA) and small nucleolar RNA (snoRNA) subtypes. We found long-lasting alterations in DNA methylation as a result of fetal alcohol exposure, specifically in the imprinted regions of the genome harboring ncRNAs and sequences interacting with regulatory proteins. The findings of this study help to expand on the mechanisms behind the long-lasting changes in the brain transcriptome of FASD individuals.
Leveraging Ingenuity for Predictive Systems Biology: An Approach To Broad-Spectrum, Host-Directed Drug Target Discovery In Infectious Diseases [50:33 minutes]
Presented By: Dr. Ramon Felciano, Co-founder and Senior Vice President, Applied Research and Partnering, QIAGEN Redwood City
Knowledge of immune system and host-pathogen pathways can inform development of targeted therapies and molecular diagnostics based on a mechanistic understanding of disease pathogenesis and the host response. We used the Ingenuity plaform to investigate the feasibility of rapid target discovery for novel broad-spectrum molecular therapeutics was investigated through comprehensive systems biology modeling and analysis of pathogen and host-response pathways and mechanisms. We used this approach to identify and prioritize candidate host targets based on strength of mechanistic evidence characterizing the role of the target in pathogenesis and tractability desiderata that include optimal delivery of new indications through potential repurposing of existing compounds or therapeutics. We will describe our approach, experimental results, and the key technology innovations now publically available in IPA.
IPA the Fast Path to Toxicity Targets of Interest [36:55 minutes]
Presented by Dr. Aaron Erdely, Health Effects Laboratory Division, NIOSH
and Kaushal Parekh, Associate Staff Ontology Engineer, QIAGEN Redwood City
Metal-rich particulate matter inhalation exposure results in
target organ toxicity but also adverse systemic effects including
cardiovascular dysfunction and immunosuppression. As a preliminary search
for induction of systemic mechanisms, generation of comprehensive
transcriptome datasets by DNA microarray, along with gene network
analysis, was performed from circulating whole blood cells, aorta, and
lung then compared to determine related biological signaling following
Also demonstrated are some exciting new features in the new 2013 IPA
Spring Release. Learn how IPA can help you quickly filter down to specific
toxicity targets of interest
IPA 2013 Spring Release [48:24 minutes]
Presented by Dr. Stuart Tugendreich, Scientific Director, IPA
The 2013 IPA Spring Release is here! Powerful new functionality enables you to upload, find, and compare datasets, and understand causal connections between diseases, genes, and networks of upstream regulators. Stuart Tugendriech, PhD, Scientific Director, IPA from QIAGEN Redwood City gives an overview of the new IPA capabilities in the release, as well as a use case utilizing the new features and how IPA helps to Discover Causal Connections. Faster.
Ingenuity Knowledge-Based Tools for Comprehensive Interpretation of Variant & Gene Expression Data [56:16 minutes]
Presented by Jean-Noel Billaud and Megan Laurance
Ingenuity Staff Scientists Jean-Noel Billaud and Megan Laurance present strategies for integrated analysis and interpretation of variant and gene expression data generated from cell lines representative of 2
breast cancer subtypes: Claudin-Low and Luminal. These subtypes represent different disease entities associated with specific molecular alterations and histo-clinical features. Interrogating these samples at both the variant and transcript level with Ingenuity's Variant Analysis and IPA software presents a powerful approach to drawing clear molecular
paths from variants and gene expression changes to phenotypes relevant to these disease subtypes including Epithelial-to-Mesenchymal Transition and Metastasis.
A Bioinformatician's Guide to Lung Cancer: Wnt7a Signaling and Beyond [40:13 minutes]
Presented by Dr. Michael Edwards, Assistant Professor at the University of Colorado Health Sciences, Denver.
This webinar discusses an important antitumor pathway in lung cancer (Wnt7a signaling) as a framework to explain the bioinformatic analysis process using IPA. Topics covered include biological function and pathway analysis, network construction, and identifying and interpreting upstream regulators.
IPA and Coronary Artery Disease: A Case Study from Harvard [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.
The Role of microRNAs in Kidneys of Hypertensive Patients [23:09 minutes]
Presented by Aimee Jackson, Ph.D.
MicroRNAs are small, non-coding RNAs that function as central regulators of gene expression and development. These regulatory molecules have been implicated in a wide range of normal and pathological activities, including embryonic development, cancer, inflammation, cardiovascular disease and viral infections. We explored the possibility that microRNA dysfunction in the kidney might contribute to hypertension, a significant health issue. We analyzed mRNA and microRNA expression profiling data from kidneys of untreated hypertensive patients and normotensive patients to identify microRNAs, microRNA targets, and gene networks that are dysregulated in hypertension. The results of these analyses identify microRNAs and their targets that could be biomarkers or therapeutic targets for hypertension.
Differential Expression of Focus Genes Associated Feed Efficiency [41:26 minutes]
Presented by Dr. Walter Bottje, Professor, Dept. of Poultry Science, University of Arkansas
Global RNA expression in breast muscle obtained from a male broiler line phenotyped for high or low feed efficiency (FE) was investigated using microarray analysis. By using an overlay function of IPA in which canonical pathways can be projected onto a set of genes, differentially expressed focus genes were identified. We selected 130 out of 260 possible canonical pathways in the IPA program that would likely be associated with normal metabolic activities and did not select those that were obviously tissue or disease specific. The results of this study provide additional insight into gene expression in muscle associated with the phenotypic expression of feed efficiency in broilers.
Scientific Webinar What You Should Know About Your 'Omics Data [58:11 minutes]
Presented by Tim Bonnert, PhD, QIAGEN Redwood City
Learn how you can now predict the cause and effect of changes in gene expression and predict the activation or inhibition of upstream molecules, such as cytokines, kinases, microRNA, receptors and many more! Included in the webinar will be an example of the biological analysis and interpretation of a gene expression data set from a study of Docetaxel Resistance in the Breast Cancer Cell Line MCF-7.
Distinct Gene Expression Profile of Regulatory T Cells in Prostate Cancer [45:00 minutes]
Presented by Simo Arredouani, Assistant Professor of Surgery at Harvard Medical School
The inhibitory role of regulatory T-cells (Tregs) in cancer is now well established. Furthermore, inhibition of Treg function has been shown both experimentally and clinically to improve the immune response towards a variety of cancers. Developing new and more effective strategies interfering with the function of Tregs in cancer requires a deep understanding of Treg suppressor machinery, and a thorough dissection of the molecular elements that orchestrate their differentiation from T cells.
A Combined Biological and Bioinformatic Analysis of Primary and Metastatic Tissues from NGS Ewing's Sarcoma Patients [58:00 minutes]
Presented by Jean-Noel Billaud, Ph.D., QIAGEN Redwood City and 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 QIAGEN Redwood City' 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 [33:44 minutes]
Presented by Darryl Gietzen, Ph.D., QIAGEN Redwood City
This webinar discusses how 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.