MetaCore

Getting Started Series (1 hour)

This seminar series is available every first Monday of the month and is designed to approach the basics. If you are just getting started or need to become reacquainted with new features, this is the series for you. Each seminar is platform centered. For example the MetaCore webinar is best for learning how to upload and analyze biological data while the MetaDrug webinar is best for starting with chemical structures. Click on the title of each topic for a detailed description of what will be covered.

Free online training is available every first Monday of the month.

United States MetaCore training at 10am PST/1pm EST

To receive invitations please email genegotraining@thomsonreuters.com.

• February 6, 2012 - Getting started with MetaCore: Getting the most from your “omics” Analysis

  
  Are you swamped with high-throughput data? Need a tool to make biological sense of it? GeneGo provides a solution for using gene/protein/miRNA/RNA/drug/metabolite lists and “omics” data to generate and prioritize hypotheses with MetaCore. This tutorial highlights:

  • How to upload data or your favorite gene list
  • How to store, share, and check data properties and signal distribution of your data
  • How to extract functional relevance using enrichment analysis and several GeneGo proprietary ontologies
  • How to prioritize your hypotheses using statistically significant enrichment histograms
  • How to overlay your data on pre-built GeneGo maps and networks
  • How to visualize drug targets, disease biomarkers, orthologs, and more on your maps and networks
  • How to generate and use an enrichment workflow report

  
  Topic: Getting started with MetaCore
  Date: February 6, 2012
  Time: San Francisco 10 am - New York 1 pm
  
  Click here to register
  
  Once the host approves your request, you will receive a confirmation email with instructions for joining the meeting.
  
  

• March 5, 2012 - How to choose the right network building or interactome algorithm to test and expand your hypothesis

  
  One aspect of systems biology is to integrate complex interactions of biological systems. GeneGo provides a highly annotated and dense interaction database with over ten different network building algorithms. Here we demonstrate the strength of these tools in the ability to visualize signaling interaction networks and expand on your hypotheses outside of the realm of your core research areas. This tutorial describes each network building algorithm and modeling workflows including building with canonical pathway interactions, with examples of when to use each. In this session we also highlight how to optimize the visualization of your interactions of interest on a network we will build. We will show tools such as how to add/ hide/show objects and how to manipulate visualizations of pathways using post-filters such as disease, tissue, orthologs or gene otology processes.
  
  Topic: How to choose the right network building algorithm
  Date: March 5, 2012
  Time: San Francisco 10 am - New York 1 pm
  
  Click here to register
  
  Once the host approves your request, you will receive a confirmation email with instructions for joining the meeting.
  
  

• April 2, 2012 - Eureka! Searching GeneGo content: EZ Search, MetaSearch and easy exporting of knowledge mining results

  
  Tired of spending hours searching the public domain to generate your research objectives? GeneGo now provides a new Google-like interface to search your favorite miRNAs, genes, proteins, diseases or compounds with just one click. In this training session you will learn:

  • How to use EZ search to find all you need to know about your favourite miRNA/gene/protein/ disease/compound
  • How to use the EZ search results to take your hypothesis further
  • How to use EZ search to find your favourite pathway
  • How to use MetaSearch to create specific search queries and generate gene lists for further analysis
  • How to export search results
  • How to report commonalities between your search and your high-throughput data

  
  Topic: Searching GeneGo content: EZ Search, MetaSearch
  Date: April 2, 2012
  Time: San Francisco 10 am - New York 1 pm
  
  Click here to register
  
  Once the host approves your request, you will receive a confirmation email with instructions for joining the meeting.
  
  

• May 8, 2012 - Discovering Target-oriented mechanisms of action

  
  One of the most common approaches of elucidating the effects of a gene or compound is to directly target this entity with various biochemical techniques including introducing competitive compounds and knocking down expression levels. As a consequence we are left with an observed phenotype with a gap in knowing how this phenotype arose. In this session we will demonstrate how to determine potential signaling mechanisms emanating from a “target” to a phenotype. We will specifically focus on exploiting the annotating interaction content, toxicology/disease/phenotypic ontologies and the shortest- path network build algorithm. Example questions you may ask when using this approach include:

  • How do I identify the mechanisms that cause toxicity “X” after targeting a receptor?
  • What are the mechanisms involved in inducing disease “X” after knock out/ over-expression of my favorite gene?
  • If I target my favorite gene I observe and increase in expression of several others. What are the mechanisms involve?
  • My drug induced cardiotoxicity and this may be an off target effect. Can I determine the molecular basis of this observation?

  
  Topic: Discovering Target-oriented mechanisms of action
  Date: May 8, 2012
  Time: San Francisco 10 am - New York 1 pm
  
  Click here to register
  
  Once the host approves your request, you will receive a confirmation email with instructions for joining the meeting.
  
  

• June 5, 2012 - How to identify microRNA targets, work with microRNA data and use predicted target information

  
  MicroRNAs (miRNAs) regulate gene expression by directly binding to messenger RNA sequences, leading to the repression of protein translation. It is has been hypothesized that identifying patterns of miRNA expression in disease states and elucidating the processes dictated by their targets will be critical for disease classification and defining mechanisms of disease progression. In this tutorial you will learn:

  • How to search for all you need to know about your miRNA (including associated targets, diseases and pathways)
  • How to exploit the expand-by-one network algorithm to visualize and export miRNA targets
  • How to use MetaLink to visualize predicted or novel miRNA targets on a network
  • How to characterize the biological functions of miRNA and their novel, known or predicted targets with GeneGo ontologies

  
  Topic: How to identify microRNA targets, work with microRNA data and use predicted target information
  Date: June 5, 2012
  Time: San Francisco 10 am - New York 1 pm
  
  Click here to register
  
  Once the host approves your request, you will receive a confirmation email with instructions for joining the meeting.
  
  

Case Study Series

This series of webinars are designed to push your hypothesis to the next step: from experimental discovery to drug targeting and clinical validation. The GeneGo platform is more than network building and enrichments and we expand on the usability here. These topics chosen are based on situations you may encounter during your analysis. They also demonstrate how to use a combination of GeneGo tools (MetaDiscovery) such as MetaCore with MetaLink or MetaDrug, Metasearch Data-mining and gene list functions, network building and interactome combinations. Attending the basic sessions is helpful but not mandatory.

Free online training is available every third Monday of the month.

United States MetaCore training at 10am PST/1pm EST

To receive invitations please email genegotraining@thomsonreuters.com.

• February 21, 2012 - Pathway Analysis of Genome-Wide Association Studies (GWAS) in Parkinson’s Disease using MetaCore

  
  Parkinson’s disease (PD) is a chronic, degenerative neurological disorder that affects one in 100 people over age 60. While the average age at onset of the disease is 60, an estimated five to ten percent of patients experience onset around age 40, and people as young as 30 can also be affected. There is no objective test or biomarker for PD so the rate of misdiagnosis can be relatively high, especially when the diagnosis is made by a non-specialist. One goal of PD research is to increase the incidence of correct diagnosis of patients. In accomplish this task researchers need a better fundamental understanding of the molecular mechanism(s) behind cell death in dopaminergic neurons. This case study aims to elucidate these mechanisms by using a pathway analysis approach to analyze data from a high-resolution, genome-wide association study (GWAS) of Parkinson’s disease.
  
  Topic: Identifying tissue specific pathologies in Parkinson’s via Parkin
  Date: February 21, 2012
  Time: San Francisco 10 am - New York 1 pm
  
  Click here to register
  
  Once the host approves your request, you will receive a confirmation email with instructions for joining the meeting.
  
  

• March 19, 2012 - Identifying ovarian cancer stem cell pathways using proteomics from serum obtained from early and late ovarian cancer mouse models.

  
  Integrated proteomic analysis of mouse cancer models and human cancer cell populations provides an innovative strategy for the identification of potential circulating cancer markers. Here, we employed a strategy that combined proteomic analysis of plasma from a mouse model of ovarian cancer (from early and late stages of tumor development) with the analysis of proteins secreted or shed by human ovarian cancer cells. To characterize the functional relevance of this set of proteins, we used pathway analysis with MetaCore and found a representation of cell adhesion, proliferation, extracellular matrix remodeling, and development/stem-cell like characteristics. We also identified TGFbeta, MMP2, p38MAPK, NFkB, and RAS as central regulatory nodes in the global network of ovarian cancer biology.
  
  Topic: Identifying ovarian cancer stem cell pathways using proteomics
  Date: March 19, 2012
  Time: San Francisco 10 am - New York 1 pm
  
  Click here to register
  
  Once the host approves your request, you will receive a confirmation email with instructions for joining the meeting.
  
  

• April 16, 2012 - Using MetaCore to explore new beneficial ingredients in toothpaste

  
  Ever wonder what how each ingredient in our daily consumer products can benefit our well being? In this WebEx will show how MetaCore can be used to explore potential new ingredients for consumer products with a focus on toothpaste. Gene expression data from periodontitis patients will be examined for potential mechanisms and effects of current treatments as well potential new ingredients for future products such as tumeric.
  
  Topic: Using MetaCore to explore new beneficial ingredients in toothpaste
  Date: April 16, 2012
  Time: San Francisco 10 am - New York 1 pm
  
  Click here to register
  
  Once the host approves your request, you will receive a confirmation email with instructions for joining the meeting.
  
  

• May 21, 2012 - Pathway Analysis of Serological Metabolite Profiles in Rheumatoid Arthritis

  
  Metabolomic data sets obtained using Chenomx NMR Suite often require additional analysis to place them in proper context. The GeneGo pathway analysis platform can help establish this context. In this tutorial we present an analysis using serological metabolic profiles from Chenomx NMR Suite, known inflammatory markers from prior studies of the K/BxN mouse model and the GeneGo platform to generate a mechanistic hypothesis for the K/BxN mouse model and Rheumatoid arthritis (RA). The basic workflow includes the following steps:

  • Use Chenomx NMR Suite to obtain serological metabolite profiles using targeted profiling
  • Integrate known inflammatory markers from previous studies of the mouse model system
  • Use the GeneGo pathway analysis platform to generate a mechanistic hypothesis for the K/BxN mouse model

  
  Topic: Pathway Analysis of Serological Metabolite Profiles in Rheumatoid Arthritis
  Date: May 21, 2012
  Time: San Francisco 10 am - New York 1 pm
  
  Click here to register
  
  Once the host approves your request, you will receive a confirmation email with instructions for joining the meeting.
  
  

• June 18, 2012 - Identifying sub-type specific breast cancers using microRNA and gene expression profiles

  
  MicroRNAs (miRNAs) regulate gene expression by directly binding to messenger RNA sequences leading to the repression of protein translation. It is has been hypothesized that identifying patterns of miRNA expression in disease states and elucidating the processes dictated by their targets will be critical for disease classification and defining mechanisms of disease progression. Here we demonstrate how to integrate two types of data, miRNA and gene expression data, to determine miRNA signatures in specific subtypes of breast cancer. We also demonstrate how to move from a list of targets to an understanding of their functional relevance and how to map gene expression to confirm miRNA-generated hypotheses.
  
  Topic: Identifying sub-type specific breast cancers using microRNA and gene expression profiles
  Date: June 18, 2012
  Time: San Francisco 10 am - New York 1 pm
  
  Click here to register
  
  Once the host approves your request, you will receive a confirmation email with instructions for joining the meeting.
  
  

  MetaDrug

Getting Started Series (1 hour)

This seminar series is available every first Monday of the month and is designed to approach the basics. If you are just getting started or need to become reacquainted with new features, this is the series for you. Each seminar is platform centered. For example the MetaCore webinar is best for learning how to upload and analyze biological data while the MetaDrug webinar is best for starting with chemical structures. Click on the title of each topic for a detailed description of what will be covered.

Free online training is available every first Monday of the month.

United States MetaDrug training at 8am PST/11am EST

To receive invitations please email genegotraining@thomsonreuters.com.

• February 6, 2012 - Getting started with MetaDrug: from compound structure to pharmacological activity

  
  Do you want to predict the activity of a new molecule, solve the mechanism of action of a compound or reposition a drug for a new indication? MetaDrug, a unique systems pharmacology suite designed for predicting therapeutic and toxic effects of compounds, can help. It combines the power of systems biology (target CVs, OMICs data analysis), the versatility of classical chemical tools (QSAR, metabolic rules) and the reliability of an industry standard manually curated knowledgebase. In this tutorial we will show:

  • How to predict metabolites for your compound (or find known metabolites in our database)
  • How to use MetaDrug to predict targets for your compound (or find known targets in the database)
  • How to use the targets to find pathways and processes affected by your compound
  • How to use MetaDrug to suggest indications and predict toxicity issues for future drugs
  • How to validate your findings and formulate new hypotheses using expression data
  • How to use MetaDrug to compare and prioritize compounds

  
  Topic: Getting started with MetaDrug
  Date: February 6, 2012
  Time: San Francisco 8 am - New York 11 am
  
  Click here to register
  
  Once the host approves your request, you will receive a confirmation email with instructions for joining the meeting.
  
  

• March 5, 2012 - MetaDrug with ToxHunter: using MetaDrug for compound safety assessment

  
  ToxHunter is a systems toxicology knowledgebase and data analysis package designed for the assessment of safety liabilities of drugs, environmental contaminants and other xenobiotics at all stages of discovery and development. ToxHunter is available as an add-on for the GeneGo MetaCore and MetaDrug systems biology and systems pharmacology solutions, and it integrates seamlessly with these products to provide a powerful tool for toxicogenomics and systems toxicology research. Log on to this webinar to learn how to:

  • Predict metabolites and identify known targets of your toxic agent
  • Apply QSAR prediction of pathological outcomes from chemical structures
  • Build toxic agent specific networks to identify the source of observed toxicity

  
  Topic: MetaDrug with ToxHunter: using MetaDrug for compound safety assessment
  Date: March 5, 2012
  Time: San Francisco 8 am - New York 11 am
  
  Click here to register
  
  Once the host approves your request, you will receive a confirmation email with instructions for joining the meeting.
  
  

• April 2, 2012 - Getting started with MetaDrug: from compound structure to pharmacological activity

  
  Do you want to predict the activity of a new molecule, solve the mechanism of action of a compound or reposition a drug for a new indication? MetaDrug, a unique systems pharmacology suite designed for predicting therapeutic and toxic effects of compounds, can help. It combines the power of systems biology (target CVs, OMICs data analysis), the versatility of classical chemical tools (QSAR, metabolic rules) and the reliability of an industry standard manually curated knowledgebase. In this tutorial we will show:

  • How to predict metabolites for your compound (or find known metabolites in our database)
  • How to use MetaDrug to predict targets for your compound (or find known targets in the database)
  • How to use the targets to find pathways and processes affected by your compound
  • How to use MetaDrug to suggest indications and predict toxicity issues for future drugs
  • How to validate your findings and formulate new hypotheses using expression data
  • How to use MetaDrug to compare and prioritize compounds

  
  Topic: Getting started with MetaDrug: from compound structure to pharmacological activity
  Date: April 2, 2012
  Time: San Francisco 8 am - New York 11 am
  
  Click here to register
  
  Once the host approves your request, you will receive a confirmation email with instructions for joining the meeting.
  
  

• May 8, 2012 - Pre-built and custom QSAR models in MetaDrug: accurate predictions from reliable data

  
  Do you want to use your assay data for predictions and save time and money for future experiments? Using a recursive partitioning algorithm, MetaDrug provides a fast and reliable approach for establishing quantitative structure-activity relationships (QSAR) for bioactive compounds. Pre-built QSAR models in MetaDrug use information from the best-in-class manually curated knowledgebase and allow you to screen compound libraries for therapeutic activity and toxic properties. Using your own data you can also build custom QSAR models in MetaDrug to leverage the experience of your lab with GeneGo tools. In this tutorial you will learn:

  • How to work with built-in QSAR models in MetaDrug
  • How to generate a training and a test set (using example data from the PubChem Assay database)
  • How to build and evaluate a newly created QSAR model
  • How to integrate QSAR prediction results into pathway analysis

  
  Topic: Pre-built and custom QSAR models in MetaDrug
  Date: May 8, 2012
  Time: San Francisco 8 am - New York 11 am
  
  Click here to register
  
  Once the host approves your request, you will receive a confirmation email with instructions for joining the meeting.
  
  

• June 5, 2012 - MetaDrug for drug repositioning: finding new indications and biomarkers for drug action monitoring

  
  Drug repositioning offers the opportunity to reduce risk and time of development when compared to de novo drug discovery. MetaDrug incorporates several algorithms to predict new indications for drugs using pathway analysis of drug targets, gene-disease associations and QSAR modeling. In the first part of the training we will demonstrate case studies on drug repositioning, including the prediction of new therapeutic activities for Vioxx®. In the second part, using the example of a novel antineoplastic agent for triple-negative breast cancer treatment, we will show how to use MetaDrug for assessing surrogate end point biomarkers (SEBs). SEBs are gaining popularity in clinical science as administered medications become more individualized and specialized, and the need to cut costs of clinical trials while providing efficient care becomes more and more apparent. In this study, we used a biologically relevant network of protein drug targets to identify proteins suitable for drug efficacy monitoring, which could help to generate rapid feedback about drug effects on the body.
  
  Topic: MetaDrug for drug repositioning: finding new indications and biomarkers for drug action monitoring
  Date: June 5, 2012
  Time: San Francisco 8 am - New York 11 am
  
  Click here to register
  
  Once the host approves your request, you will receive a confirmation email with instructions for joining the meeting.
  
  

  DataRanger

United States training at 9am PST/12pm EST

To receive invitations please email genegotraining@thomsonreuters.com.

• February 18, 2011 - DataRanger Introductory Webinar

  
  

  • Are you still managing your data in Excel?
  • Need an easy way to tether metadata to your experiments?
  • Want to process and annotate files without having to be a stats expert or learning complicated software?
  
  DataRanger can help with all this and more.it will take you from what the data .is. to what the data .means. in just MINUTES!
  
  DataRanger is a user-friendly wizard that will manage, annotate, and statistically process your data.
  
  It allows you to easily:
  • start with your raw data or a .soft file from GEO
  • breeze through annotation and file organization steps with our controlled vocabulary terms or add your own
  • normalize and process files, FDR, filtering, DEG, and GSEA
  • get your data with all the parameters saved in the Data Manager space in MetaCore
  • or launch a MetaCore analysis workflow immediately at the last step
  
  
  

In addition to having the option of attending full day courses off-site, you can arrange for a course on-site catered to your analysis and group needs. Options include any on or a combination of the following:

1. 3 hour basic MetaCore:
   • Uploading data : expression profiles of genes, proteins, siRNAs, miRNAs etc.
   • EZ start interface
   • EZ Search: one-stop-shop data mining tool for access to your favorite gene, disease, protein, drug, map, network or article
   • Enrichment Analysis: determine the most representative process for your data across nine GeneGo ontologies and three Gene Ontology categories
2. 3 hour advanced MetaCore
   • Network algorithms: Learn which algorithm out of the 10 best suits your analysis needs
   • Interactome: determine categorical connectivity for your geneg list or your favorite protein
   • MetaSearch: extract lists of genes, proteins, compounds, biomarkers using Boolean query searches for seamless analysis with MetaCore
3. 3 hour MetaDrug
   • Uploading structures
   • Predicting metabolites and similar structures
   • Predicting activity with our extensive QSAR list or create your own
   • Identify targets for your compound and predicted metabolites
   • Pathway and enrichment analysis of targets
4. 3 hour MetaCore/MetaDrug combination
   • Dual approach analysis:
     • start with genes and identify targets then determine potential target pathways and toxicity
     • start with compounds and map target pathways to overlay expression data to validate or rule out drug effects and toxicity predictions
5. Scheduled 1 on 1 project consultations
6. Diseases or application specific seminar presentations (similar to Bench to bedside Webinars )
7. GeneGo Module oriented
   • Enrichment and comparative analysis (1 hr)
   • Interactome and Network building (1 hr)
   • Data mining Gene list function (1 hr)
   • Biomarker assessment (1 hr)
   • Networks and MapEditor

Cost: $2,500 per day plus expenses.

Includes training materials (here).