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Quick Start Guide to Running Ingenuity Pathway Analysis (IPA)
 
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In this video, we will discuss how to quickly get started running an IPA core analysis. This includes uploading external data, formatting it to work with IPA, and setting filters on gene features. I was not able to find a quick-start guide to IPA, and I am often asked about how to upload data, so I decided to create this video. I hope it is helpful. I welcome comments and feedback below. Iowa Institute of Human Genetics: https://medicine.uiowa.edu/humangenetics/ Visit my website: www.michaelchimenti.com Follow me on twitter: @ChimentiMichael
LIVE MSI Tutorial: Ingenuity Pathway Analysis (IPA) New User Training 4/24/18
 
02:55:30
IPA is a powerful analysis and search tool that uncovers the significance of omics data and identifies new targets or candidate biomarkers within the context of biological systems. If you're working with ‘omics experiments, such as RNA-seq, small RNA-seq, microarrays including miRNA and SNP, metabolomics and proteomics, you should be using IPA. Date: 4/28/18 Learn more at https://www.msi.umn.edu
Views: 991 UofMMSI
Bioinformatics analysis on IPA (part 1): functions and pathways
 
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This video serves as a hands-on tutorial that expands on the bioinformatics themes presented in the lecture, "Understanding Bioinformatics: Finding the Biology in a List of Genes". The example data set was obtained by taking the top 1000 transcripts correlated (Spearman) to lung cancer stage in a publicly-available gene expression study (GEO#GSE41271). This tutorial was recorded as part of a lecture series given to a class of high school students at GVR Denver School of Science and Technology as part of their senior class project.
Views: 8103 Michael Edwards
2019 Ingenuity Pathway Analysis Workshop
 
04:39:09
Ingenuity Pathway Analysis (IPA) is a commercial pathway and network analysis tool for systems biology analysis. Access to an institutional license for IPA is administered by the Research Informatics Core (RIC) and the Research Resources Center (RRC). IPA applications include: Pathway enrichment analysis Network building Biomarker discovery Elucidation of biological mechanisms Visualization of complex trends Hypothesis generation Literature review A Qiagen IPA representative will be offering this FREE hands-on training workshop.
IPA Data Analysis Part 1
 
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This session focus on formatting your own data and the best practices to analyze them in IPA. Topics include: - Format the incoming data to be analyzed by IPA - Upload the data to be analyzed - Set filter parameters and other core setting options - Run analysis
Views: 30899 Ingenuity Web Apps
Ingenuity Pathway Analysis: Regulator Effects Analysis
 
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Regulator Effects feature in IPA provides insights into your data by integrating Upstream Regulator results with Downstream Effects results to create causal hypotheses that explain what may be occurring upstream to cause particular phenotypic or functional outcomes downstream.
Views: 1165 Ingenuity Web Apps
IPA Downstream Effects Analysis
 
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IPA's downstream effects analysis is a whole new way to visualize biological trends in your experiment. Predict an increase or decrease in downstream biological processes to explain the effect of disregulated genes from your experiment.
Views: 925 Ingenuity Web Apps
Bioinformatics analysis on IPA (part 3): comparison analysis.
 
04:48
This video serves as a hands-on tutorial that expands on the bioinformatics themes presented in the lecture, "Understanding Bioinformatics: Finding the Biology in a List of Genes". The example data set was obtained by taking the top 1000 transcripts correlated (Spearman) to lung cancer stage in a publicly-available gene expression study (GEO#GSE41271). This tutorial was recorded as part of a lecture series given to a class of high school students at GVR Denver School of Science and Technology as part of their senior class project.
Views: 2282 Michael Edwards
Ingenuity Pathway Analysis (IPA)-OmicSoft integration
 
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Secondary analysis in Array Studio (training session) of RNA-seq data *Find differentially-expressed genes/transcripts *Send the data to IPA Biological interpretation of the whole transcriptome *Analyze non-responder versus responder gene expression signatures to pinpoint significant genes and pathways associated with advanced melanoma *Identify significantly differentially expressed isoforms and their association to advanced melanoma (IsoProfiler-GTEx) *Generate novel regulatory networks as hypotheses suggesting drivers of the expression changes observed in the innate anti-PD1 resistance treatment in advanced melanoma. *Compare this analysis across a repository of processed datasets from OmicSoft Lands (Analysis Match) *Visualize a specific gene of interest in OncoLand Session Leader: Dr. Jean-Noel Billaud, Senior Principal Scientist, QIAGEN Bioinformatics
Views: 145 OmicsoftCorporation
Ingenuity Pathway Analysis: Molecule Activity Predictor (MAP)
 
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A Short video to help explain IPA new feature MAP. Using this feature one can Interrogate sub-networks and Canonical Pathways and generate hypotheses by selecting a molecule of interest, indicating up or down regulation, and simulating directional consequences of downstream molecules and the inferred activity upstream in the network or pathway
Views: 3698 Ingenuity Web Apps
Spring IPA 2014
 
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The 2014 Spring Release of QIAGEN's Ingenuity Pathway Analysis (IPA®) has exciting new capabilities including Regulator Effects and expanded My Findings. With IPA's newest features you can quickly distill the information in your data to understand upstream regulatory mechanisms and their connections to downstream functional effects generating testable hypotheses.
Views: 571 Ingenuity Web Apps
3 Approaches to Pathway Analysis
 
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In this video we describe the three classical approaches to pathway analysis, the pros and cons of each approach, and the types of insights one can make based on the approach used.
FunctBioinfo2016_Day3pt6_FindingTheKeyPlayersInEMTsignalingDifference-Dusp1
 
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Lecture for bioengineering graduate students in BIOE 5420, Functional Bioinformatics, given on Day 3 (02/10/16) of the course. In these series of videos, we use Ingenuity Pathway Analysis (IPA) to find the biological meaning in genes that change due to cell state (pluripotent vs.embryonic) and day (differentiated vs. stem cell) in GEO study # GSE27087.
Views: 157 Michael Edwards
Bioinformatics analysis on IPA (part 2): networks, upstream regulators and regulatory networks.
 
14:38
This video serves as a hands-on tutorial that expands on the bioinformatics themes presented in the lecture, "Understanding Bioinformatics: Finding the Biology in a List of Genes". The example data set was obtained by taking the top 1000 transcripts correlated (Spearman) to lung cancer stage in a publicly-available gene expression study (GEO#GSE41271). This tutorial was recorded as part of a lecture series given to a class of high school students at GVR Denver School of Science and Technology as part of their senior class project.
Views: 3733 Michael Edwards
Introduction to Pathway and Network Analysis of Gene Lists
 
01:24:27
This is the first module in the 2016 Pathway and Network Analysis of -Omics Data workshop hosted by the Canadian Bioinformatics Workshops. This lecture is by Gary Bader from the University of Toronto. How it Begins by Kevin MacLeod is licensed under a Creative Commons Attribution license (https://creativecommons.org/licenses/by/4.0/) Source: http://incompetech.com/music/royalty-free/index.html?isrc=USUAN1100200 Artist: http://incompetech.com/
Views: 17190 Bioinformatics DotCa
IPA: Causal Network Analysis & Upstream Regulator Analysis
 
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Predict upstream molecules, including microRNA and transcription factors, which may be causing the observed gene expression changes.
Views: 2253 Ingenuity Web Apps
Pathway Activity Analysis
 
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Identify significant scientific discoveries from more than just an enrichment p-value; quickly predict if Canonical Pathways are increased or decreased based on differentially expressed genes or proteins in your dataset.
Views: 3553 Ingenuity Web Apps
Correlation Engine (NextBioR) and IPA workshop pt4: IPA pathway function
 
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The Health Sciences Library’s Informatics Workshop Series presents: NextBio and IPA: Using commercial bioinformatics platforms to answer biological questions. This workshop was lead by Dr. Michael Edwards, assistant professor of medicine at UC Denver on May 19, 2016. The goals of this workshop is for the audience to be able to: • Identify the resources available on the commercial bioinformatics platforms NextBio Research and Ingenuity Pathway Analysis (IPA). • Understand how public and commercial bioinformatics tools and databases can advance your research without requiring your own data to analyze. • Understand the utility of these tools on real data through a real time demonstration of NextBio Research and IPA using your questions.
Views: 338 Michael Edwards
What Is IPA Analysis?
 
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"What Is IPA Analysis? Watch more videos for more knowledge IPA Data Analysis Part 1 - YouTube https://www.youtube.com/watch/DtxqK_nL4lw What Is IPA Research? - YouTube https://www.youtube.com/watch/5ooZdp9AB9M What Is IPA Analysis? - YouTube https://www.youtube.com/watch/kT3deFGvzB4 Quick Start Guide to Running Ingenuity Pathway ... https://www.youtube.com/watch/ub7GLpD8dPQ Comparison Analysis in IPA - YouTube https://www.youtube.com/watch/mmCSRdudMY4 Interpretative Phenomenological Analysis by ... https://www.youtube.com/watch/72B7nbYRAOs Bioinformatics analysis on IPA (part 1): functions ... https://www.youtube.com/watch/1sCa-lS1ERY LIVE MSI Tutorial: Ingenuity Pathway Analysis (IPA ... https://www.youtube.com/watch/vnpSkANL2no Introduction to IPA (2008) - YouTube https://www.youtube.com/watch/5JC-DciAr5Q 3 Approaches to Pathway Analysis - YouTube https://www.youtube.com/watch/t90x9TlW6Y0 Bioinformatics analysis on IPA (part 3): comparison ... https://www.youtube.com/watch/RmcJTXwR00M Coding Part 1: Alan Bryman's 4 Stages of ... https://www.youtube.com/watch/7X7VuQxPfpk Phenomenological Research: Qualitative Analysis ... https://www.youtube.com/watch/4EeWyAI0q7Y IPA: Causal Network Analysis & Upstream ... https://www.youtube.com/watch/XV8tuaLU1_w Pathway Activity Analysis - YouTube https://www.youtube.com/watch/uBAo2iBax48 LIVE MSI Tutorial: Ingenuity Pathway Analysis (IPA ... https://www.youtube.com/watch/LPPagTqHkuw Comparison Analysis in IPA - YouTube https://www.youtube.com/watch/G9MVM22f2OI IPA Downstream Effects Analysis - YouTube https://www.youtube.com/watch/II1F1xOh1io Ingenuity Variant Analysis New User Training July ... https://www.youtube.com/watch/8SymeM2B2xg 11. Introduction to Methods of Qualitative Research ... https://www.youtube.com/watch/LLjKdvVzKXM"
Views: 1858 Ask Question II
Using IPA to analyze RNA-Seq data in Alzheimer's Disease
 
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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.
Views: 5159 Ingenuity Web Apps
Are You Getting The Most Out Of Your Data?
 
01:03:01
You know IPA is a powerful application for you to analyze and interpret your 'omics data. But are you getting all you can out of your data with IPA? We want to show you how IPA can help you go beyond pathway analysis and uncover novel insights in your data. In collaboration with Dr. Bhaumik B. Patel from Virginia Commonwealth University, Dr. Jean-Noel Billaud from QIAGEN went further into IPA to discover even more within the data. The research is focused on understanding the role of cancer stem or stem-like cells (CSC) in carcinogenesis, specifically, colorectal carcinogenesis and developing therapies that selectively target these cells.
Views: 372 Ingenuity Web Apps
Regulator Effects
 
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The Regulator Effects analysis in IPA provides unprecedented insights into your data by integrating Upstream Regulator results with Downstream Effects results to create causal hypotheses that explain what may be occurring upstream to cause particular phenotypic or functional outcomes downstream
Views: 628 Ingenuity Web Apps
Comparison Analysis in IPA
 
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Comparison Analysis enables visualization of IPA analysis results across multiple conditions. For example, across your datasets representing different compound doses, a time course, or other conditions you have analyzed to identify trends, similarities, and differences in their predicted effects on pathways, upstream regulators, and diseases and functions. This short video provides a brief overview of the comparison analysis capability in IPA
Views: 2412 Ingenuity Web Apps
Learn how to use IPA's microRNA Target Filter
 
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Learn how to use IPA's microRNA Target Filter through a live demonstration and also about IPA's extensive microRNA content (Sept. 2011). The microRNA Target Filter helps you quickly identify and prioritize microRNA targets, and includes both RNA-RNA interactions and expression values. IPA has the only commercially available microRNA Target Filter that allows you upload, analyze, prioritize, filter, and visualize microRNA-mRNA relationships, all within a single tool!
Views: 3322 Ingenuity Web Apps
Using IPA to explore microRNA impacts on molecular mechanisms of disease
 
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In the rapidly evolving field of microRNA research, which still relies heavily on a variety of measurement techniques and prediction algorithms for target identification, the challenge is in identifying the most biologically relevant targets. To identify potential microRNA markers for disease progression from primary melanoma to metastatic melanoma, Ingenuity scientists applied biological information to prioritize mRNA targets, understand how these biomarker candidates contribute to disease progression, and design followup experiments to test their hypotheses. IPA®'s new microRNA Target Filter functionality enables prioritization of experimentally validated and predicted mRNA targets through the addition of biological information from the Ingenuity Knowledge Base and the ability to include experimental results in a single application.
Views: 2963 Ingenuity Web Apps
Correlation Engine (NextBioR) and IPA workshop pt2: using NextBioR to analyze by phenotype
 
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The Health Sciences Library’s Informatics Workshop Series presents: NextBio and IPA: Using commercial bioinformatics platforms to answer biological questions. This workshop was lead by Dr. Michael Edwards, assistant professor of medicine at UC Denver on May 19, 2016. The goals of this workshop is for the audience to be able to: • Identify the resources available on the commercial bioinformatics platforms NextBio Research and Ingenuity Pathway Analysis (IPA). • Understand how public and commercial bioinformatics tools and databases can advance your research without requiring your own data to analyze. • Understand the utility of these tools on real data through a real time demonstration of NextBio Research and IPA using your questions.
Views: 207 Michael Edwards
FunctBioinfo2016_Day3pt1_ReviewOfStudy-IPAoverview
 
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Lecture for bioengineering graduate students in BIOE 5420, Functional Bioinformatics, given on Day 3 (02/10/16) of the course. In these series of videos, we use Ingenuity Pathway Analysis (IPA) to find the biological meaning in genes that change due to cell state (pluripotent vs.embryonic) and day (differentiated vs. stem cell) in GEO study # GSE27087.
Views: 145 Michael Edwards
Introduction to Pathway and Network Analysis of Gene Lists
 
01:24:49
This is the first module of the Pathway and Network Analysis of -omics Data 2018 workshop hoste by the Canadian Bioinformatics Workshops at the Ontario Institute for Cancer Research. This session is by Gary Bader from the University of Toronto.
IPA Transcription Factor Analysis
 
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IPA's transcription factor analysis is a novel approach to transcription factor prediction. Predict activation or inhibition of transcription factors to explain gene expression changes in your data set.
Views: 3469 Ingenuity Web Apps
RNA-Seq analysis in ArrayStudio and biological interpretation in IPA
 
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RNA-Seq profiling and analysis of pre-treatment melanomas in Array Studio. Manage sample data QC and align Quantify and visualize expression Find differentially-expressed genes/transcripts (anti-PD1 non-responders vs. responders) Send the data to IPA Biological Interpretation of the transcriptome in Ingenuity Pathway Analysis (IPA) Analyze expression signatures to pinpoint significant pathways associated with advanced melanoma Identify differentially expressed splice variants and their association to advanced melanoma Generate novel regulatory networks as hypotheses suggesting drivers of anti-PD1 resistance in advanced melanoma. Session Leader: Dr. Joseph Pearson, Head of customer Support, QIAGEN Bioinformatics Session Leader: Dr. Jean-Noel Billaud, Senior Principal Scientist, QIAGEN Bioinformatics
FunctBioinfo2016_Day3pt9_UpstreamRegulatorsAndNetworksInIPA
 
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Lecture for bioengineering graduate students in BIOE 5420, Functional Bioinformatics, given on Day 3 (02/10/16) of the course. In these series of videos, we use Ingenuity Pathway Analysis (IPA) to find the biological meaning in genes that change due to cell state (pluripotent vs.embryonic) and day (differentiated vs. stem cell) in GEO study # GSE27087.
Views: 293 Michael Edwards
FunctBioinfo2016_Day3pt8_NetworksAndOverlayingPathwaysFunctions
 
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Lecture for bioengineering graduate students in BIOE 5420, Functional Bioinformatics, given on Day 3 (02/10/16) of the course. In these series of videos, we use Ingenuity Pathway Analysis (IPA) to find the biological meaning in genes that change due to cell state (pluripotent vs.embryonic) and day (differentiated vs. stem cell) in GEO study # GSE27087.
Views: 602 Michael Edwards
AACR Workshop 2014_IPA-1_UploadingData
 
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IPA_Part1: A series of video tutorials that complement the "Using Genomics and Bioinformatics in Cancer Research" laboratory for the 23rd Annual AACR Workshop: Molecular Biology in Clinical Oncology. This tutorial covers importing a gene list into the bioinformatics platform Ingenuity Pathway Analysis (IPA) (http://www.ingenuity.com/).
Views: 448 Michael Edwards
AACR Workshop 2014_IPA-4_Networks
 
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IPA_Part4: A series of video tutorials that complement the "Using Genomics and Bioinformatics in Cancer Research" laboratory for the 23rd Annual AACR Workshop: Molecular Biology in Clinical Oncology. This tutorial covers functions and applications associated with the Network tab in the bioinformatics platform Ingenuity Pathway Analysis (IPA) (http://www.ingenuity.com/).
Views: 285 Michael Edwards
BigDataBioinfo_Day4_LoadingGeneListIntoIPA
 
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Video is an introduction to the bioinformatics platform Ingenuity Pathway Analysis (Qiagen) given to high school seniors in the ‘Big Data’ course at GVR DSST. We import our gene lists related to stage 3 breast cancer that we created using NextBio Research into IPA to find their biological connections (907 genes total). I would like to thank the people at Ingenuity Systems/Qiagen (Dr. Stuart Tugendreich in particular) for donating the use of their platform for this course.
Views: 28 Michael Edwards
FunctBioinfo2016_Day3pt7_Pathways-AddingGenesInIPA
 
06:12
Lecture for bioengineering graduate students in BIOE 5420, Functional Bioinformatics, given on Day 3 (02/10/16) of the course. In these series of videos, we use Ingenuity Pathway Analysis (IPA) to find the biological meaning in genes that change due to cell state (pluripotent vs.embryonic) and day (differentiated vs. stem cell) in GEO study # GSE27087.
Views: 130 Michael Edwards
AACR Workshop 2014_IPA-3_DiseasesAndFunctions
 
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IPA_Part1: A series of video tutorials that complement the "Using Genomics and Bioinformatics in Cancer Research" laboratory for the 23rd Annual AACR Workshop: Molecular Biology in Clinical Oncology. This tutorial covers functions and applications associated with the Disease and Function tab in the bioinformatics platform Ingenuity Pathway Analysis (IPA) (http://www.ingenuity.com/).
Views: 225 Michael Edwards
BioProfiler
 
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Quickly profile a disease or phenotype by understanding its associated genes and compounds. Identify genes known to be causally relevant as potential targets or identify targets of toxicity, associated known drugs, biomarkers and pathways.
Views: 560 Ingenuity Web Apps
IPA Webinar West Nile Virus - Leveraging IPA and RNA-seq Data For Infectious Disease Research
 
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IPA is a powerful application for you to analyze and interpret your 'omics data. We want to show you how IPA can help you go beyond pathway analysis and uncover novel insights in RNA-seq data. Infection by West Nile Virus (WNV) is a worldwide public health concern, being the most common cause of epidemic viral encephalitis in USA, yet the viral pathogenesis is not well understood. Using QIAGEN Ingenuity Pathway Analysis’ features, we were able to shed light on canonical pathways, biological processes as well as transcriptional regulators involved in WNV infection. Using data from RNA sequencing, we analyzed the transcriptome of primary human macrophages of 10 healthy donors infected in vitro with WNV. Dr. Stuart Tugendreich, Scientific Director for IPA, presents this informative case study leveraging QIAGEN's Bioinformatics solutions.
Views: 1050 Ingenuity Web Apps
Correlation Engine (NextBioR) and IPA workshop pt6: upstream regulators and regulatory networks
 
09:28
The Health Sciences Library’s Informatics Workshop Series presents: NextBio and IPA: Using commercial bioinformatics platforms to answer biological questions. This workshop was lead by Dr. Michael Edwards, assistant professor of medicine at UC Denver on May 19, 2016. The goals of this workshop is for the audience to be able to: • Identify the resources available on the commercial bioinformatics platforms NextBio Research and Ingenuity Pathway Analysis (IPA). • Understand how public and commercial bioinformatics tools and databases can advance your research without requiring your own data to analyze. • Understand the utility of these tools on real data through a real time demonstration of NextBio Research and IPA using your questions.
Views: 161 Michael Edwards
Correlation Engine (NextBioR) and IPA workshop pt5: IPA functions and networks
 
07:14
The Health Sciences Library’s Informatics Workshop Series presents: NextBio and IPA: Using commercial bioinformatics platforms to answer biological questions. This workshop was lead by Dr. Michael Edwards, assistant professor of medicine at UC Denver on May 19, 2016. The goals of this workshop is for the audience to be able to: • Identify the resources available on the commercial bioinformatics platforms NextBio Research and Ingenuity Pathway Analysis (IPA). • Understand how public and commercial bioinformatics tools and databases can advance your research without requiring your own data to analyze. • Understand the utility of these tools on real data through a real time demonstration of NextBio Research and IPA using your questions.
Views: 197 Michael Edwards
Pathway Analysis
 
04:18
A brief description of the Reactome pathway analysis tool. The tool allows you to analyze a list of protein, gene, expression data or compound identifiers and determine how they are likely to affect pathways.
Views: 15830 Reactome Knowledgebase
AACR Workshop 2014_IPA-2_CanonicalPathways
 
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IPA_Part1: A series of video tutorials that complement the "Using Genomics and Bioinformatics in Cancer Research" laboratory for the 23rd Annual AACR Workshop: Molecular Biology in Clinical Oncology. This tutorial covers functions and applications associated with the Pathway tab in the bioinformatics platform Ingenuity Pathway Analysis (IPA) (http://www.ingenuity.com/).
Views: 395 Michael Edwards
Correlation Engine (NextBioR) and IPA workshop pt7: closing statements and questions
 
06:11
The Health Sciences Library’s Informatics Workshop Series presents: NextBio and IPA: Using commercial bioinformatics platforms to answer biological questions. This workshop was lead by Dr. Michael Edwards, assistant professor of medicine at UC Denver on May 19, 2016. The goals of this workshop is for the audience to be able to: • Identify the resources available on the commercial bioinformatics platforms NextBio Research and Ingenuity Pathway Analysis (IPA). • Understand how public and commercial bioinformatics tools and databases can advance your research without requiring your own data to analyze. • Understand the utility of these tools on real data through a real time demonstration of NextBio Research and IPA using your questions.
Views: 134 Michael Edwards
Discovering Cellular Mechanisms and Markers in Anti-PD1 Non-Responders Through Ingenuity Pathway..
 
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Presented At: Cancer Research & Oncology 2018 Presented By: Devendra Mistry, PhD - Senior Field Application Scientist, Bioinformatics, QIAGEN Speaker Biography: Devendra (Dev) received his PhD from University of California San Diego(UCSD) Biomedical Sciences graduate program and did postdoctoral studies under both academic and pharmaceutical settings. During his post-doctoral studies, he focused on cellular mechanisms regulating stem cells and cancer stem cells through next-gen sequencing data generation, analysis, interpretation and mining. Dev joined QIAGEN as a field application scientist in 2015. In the past 3 years, he has provided trainings to many pharma, biotech, academic and government investigators for different QIAGEN bioinformatics software. In addition, he has helped many of these users troubleshoot problems with their existing workflows and design new workflows. Webinar: Discovering Cellular Mechanisms and Markers in Anti-PD1 Non-Responders Through Ingenuity Pathway Analysis and Oncoland Webinar Abstract: In the last two decades, large amount of next-generation sequencing (NGS) and -omics data has been generated in the field of immuno-oncology. Generating hypotheses by analyzing hundreds if not thousands of differentially expressed genes from expression studies and mining information from large amount of publicly available NGS and -omics data can be a very daunting task. QIAGEN’s Oncoland/Arraystudio (from Omicsoft) and Ingenuity Pathway Analysis (IPA) software provide with a set of tools and functionalities to do analysis and interpretation of NGS data to generate meaningful hypotheses and the ability to mine and compare information across a very large number of datasets curated from publicly available from sources such as GEO, SRA, TCGA, GTEX and others. In this webinar, we use gene expression data from a clinical study (GSE67501) focused on understanding the mechanism underlying anti-PD-1 therapy failure in advanced renal cell carcinoma patients. Using this data and the data curated from TCGA and other sources, it will be demonstrated how Arraystudio and Ingenuity Pathway Analysis can be used to generate hypotheses for mechanism of action and to discover potential targets and biomarkers. Learning Objectives: 1. Introduction to databases backing Ingenuity Pathway Analysis and Oncoland 2. Studying potential biomarkers and targets through Oncoland’s data mining and comparison tools 3. Generation of peer-reviewed literature backed hypotheses through Ingenuity Pathway Analysis Earn PACE/CME Credits: 1. Make sure you’re a registered member of LabRoots (https://www.labroots.com/virtual-event/cancer-research-oncology-2018) 2. Watch the webinar on YouTube above or on the LabRoots Website (https://www.labroots.com/virtual-event/cancer-research-oncology-2018) 3. Click Here to get your PACE (Expiration date – October 11, 2020 09:00 AM)– https://www.labroots.com/credit/pace-credits/3096/third-party LabRoots on Social: Facebook: https://www.facebook.com/LabRootsInc Twitter: https://twitter.com/LabRoots LinkedIn: https://www.linkedin.com/company/labroots Instagram: https://www.instagram.com/labrootsinc Pinterest: https://www.pinterest.com/labroots/ SnapChat: labroots_inc
Views: 63 LabRoots
Comparison Analysis in IPA
 
02:04
Views: 214 QIAGEN
Ingenuity Variant Analysis Overview
 
03:47
Ingenuity Variant Analysis combines analytical tools and integrated content to help you rapidly identify and prioritize variants by drilling down to a small, targeted subset of compelling variants based both upon published biological evidence and your own knowledge of disease biology. With Variant Analysis, you can interrogate your variants from multiple biological perspectives, explore different biological hypotheses, and identify the most promising variants for follow-up.
Views: 2455 Variant Analysis
SCvsNorm_BloodCells_RNAexpress_4of7studies_pt3_IPA
 
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Videos describe the bioinformatics results from the 1142 genes differentially expressed in at least 4 out of 7 global RNA expression studies that compared blood cells from sickle cell subjects to control subjects in the Correlation Engine database (Illumina). Genes upregulated/downregulated due to sickle cell were found to contain more than the expected members associated with viral replication, and the pattern of expression indicates an inhibitory effect on this process. I also identify 50 genes (with BNIP3L being at the top of the list) that produce changes in the transcriptome that are positively or negatively correlated to the changes due to sickle cell when knocked out. I also uploaded the 1142 genes from the meta-analysis into the bioinformatics platform, Ingenuity Pathway Analysis (IPA). Results from IPA confirm the presence of a gene transcription program suggesting decreased viral replication and the activity of BNIP3L affecting our genes of interest. Surprisingly, the actual transcription of BNIP3L goes up in 6 of the 7 studies even though its targets suggest decreased activation, presenting the possibility of a mutation modulating activity. I also note that the gene ABCB6 is upregulated in 5 of 7 studies but shows a decreased activity pattern on its targets that is similar to BNIP3L. An excel file containing all meta-analysis results from the 7 gene lists (1st tab) and the 1142 genes common to at least 4 out of 7 lists with median fold change (2nd tab) can be found at this link: https://drive.google.com/open?id=0B4kxx5VqjCBsek84SVU0czFMdEE A network diagram for the two master regulators (ABCB6 and BNIP3L) with their targets and connections to the anemia phenotype can be found at this link: https://drive.google.com/open?id=0B4kxx5VqjCBsNjZIY2JOU1ZHdk0 Feel free to post any questions/comments down below. I support keeping information free and available to the general public.
Views: 58 Michael Edwards
IPA_Part 2_06.13_JD
 
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IPA is software that helps researchers model, analyze, and understand the complex biological and chemical systems at the core of life science research. IPA has been broadly adopted by the life science research community and is cited in thousands of peer-reviewed journal articles. IPA helps you understand complex 'omics data at multiple levels by integrating data from a variety of experimental platforms and providing insight into the molecular and chemical interactions, cellular phenotypes, and disease processes of your system. IPA provides insight into the causes of observed gene expression changes and into the predicted downstream biological effects of those changes.
Views: 7284 Ingenuity IPA
Correlation Engine (NextBioR) and IPA workshop pt3: uploading gene lists into NextBioR
 
14:21
The Health Sciences Library’s Informatics Workshop Series presents: NextBio and IPA: Using commercial bioinformatics platforms to answer biological questions. This workshop was lead by Dr. Michael Edwards, assistant professor of medicine at UC Denver on May 19, 2016. The goals of this workshop is for the audience to be able to: • Identify the resources available on the commercial bioinformatics platforms NextBio Research and Ingenuity Pathway Analysis (IPA). • Understand how public and commercial bioinformatics tools and databases can advance your research without requiring your own data to analyze. • Understand the utility of these tools on real data through a real time demonstration of NextBio Research and IPA using your questions.
Views: 151 Michael Edwards

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