Ingenuity Systems e-Insider

Feature Highlight: Search and Explore

IPA's Search & Explore features let you quickly access robust and accurate biological and chemical information, and then apply it to answering a question or establishing a hypothesis. Many customers are using search and explore workflows to identify gene products that may be useful as tools for discriminating between one disease and another. To see this workflow, click here.

Over 500 Publications Now Cite IPA

There has been significant growth in the number of peer-reviewed original research articles that cite IPA. In 2005, 100 publications cited IPA. By 2006, the number of publications citing IPA had increased to 300. As of the publication of this newsletter, IPA has now been cited in over 500 publications. Check out the new "Search Pubs" feature that allows you to find articles relevant to your own research using key word searches at:http://www.ingenuity.com/library/search-pub.html

IPA Updates

 

  

Metabolomics (or metabolic profiling), the study of small molecule chemicals (metabolites) generated by an organism, is an emerging research area that is now becoming integrated into many life science disciplines to broaden and strengthen the drug discovery and development process. IPA's analysis and interpretation of datasets generated from the endogenous metabolome, in combination with existing capabilities, such as proteomics, and transcriptomic data analysis, will provide researchers with useful insight into the molecular mechanisms of disease and drug response that will further improve the efficiency and success of drug development. Analysis and interpretation of metabolomics dataset is now available in the latest version of IPA.
Try it now.

In early July, Ingenuity released an update to the IPA content with expansion of ligand-receptor interactions, additional protein localization content, chemical content, and toxicity categories. The additional chemical content enables better understanding and visualization of toxicity and efficacy information associated with compounds. IPA's growing library of toxicity pathways and gene lists describes functional gene groupings based on critical biological processes and key toxicological responses.

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New IPA Plug-Ins

 

These two new IPA plug-ins (Beta) allow you to quickly and easily search for knowledge within IPA directly from your web browser. From any webpage, you can highlight a gene, drug, or function name on the page and right-click with your mouse to search within IPA for genes or chemicals associated with that term. Or, you can install various IPA searches directly into your browser's search toolbar.
New IPA Plugins enable quick searches for content in IPA. Click here to access them.

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Publications - Focus on Proteomics Data Analysis and Interpretation

 

  

Over the past year, there has been a significant and steady increase in the number of publications in which researchers employ IPA as part of their proteomics workflows. To date, there have been over 500 publications using IPA. These studies utilize a number of proteomics methods (phosphoprotein chips, mass spec, 2D gel electrophoresis, and SILAC) and span a number of research areas, including investigative toxicology, biomarker discovery, diabetes, neurodegenerative disorders, and infectious diseases.

To learn how your peers are using Proteomics and IPA to further their research goals, please see the recent publications highlighted below:

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Introducing the IPA Certification Program

 

  

Ingenuity Systems is offering an on-line course for users to receive in-depth training in the Ingenuity Pathways Analysis application. The certification program provides a structured curriculum that guides users in the basic, as well as advanced, features of IPA. This training also gives users a detailed understanding of the algorithms, content and mechanics behind IPA. Upon successful completion of the course, users become officially certified in IPA.

For more information on the IPA Certification Program or to enroll, please contact Customer Support at support@ingenuity.com.

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Feature Highlight: Search & Explore

 

  

IPA's Search & Explore features make it very easy to identify sets of genes that are implicated in related but different diseases. Many of our customers are using the following workflow to identify gene products that may be useful as tools for discriminating between one disease and another. In this example, Search and Build features are used to rapidly identify genes that play a role in both Crohn's Disease and Ulcerative Colitis.

  • Step 1: Search for Genes involved in Crohn's Disease; Add genes to new My Pathway; Connect Crohn's Genes.
  • Step 2: Search for Genes involved in Ulcerative Colitis (UC); Add genes to same My Pathway; Connect UC Genes.
  • Step 3: Select Overlay Menu to Overlay Functions and Diseases. Select Crohn's Disease and Ulcerative Colitis
    under the Digestive System Disorders. Note that many of the genes involved in UC are also implicated in Crohn's Disease.

Use of IPA's Search and Explore function to identify genes that play a role in Crohn's Disease and Ulcerative Colitis.

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IPA Quick Tips

 

  

Do you want to identify the shortest molecular path between two genes or chemicals of interest?

IPA's Path Explorer tool is an excellent way to identify novel paths between genes of interest (for example, known drug targets and genes newly implicated in a disease). This tool is located under the "Build" menu available on any Network, Pathway, or Neighborhood (see screenshots below). Put one gene or chemical (node), or group of nodes, in Set A, and the other node (or group of nodes) in Set B. Set the parameters of how you would like to calculate the shortest path (you can be very general or specific about the types of molecular events used to connect these genes ), then click "Apply". A table will be displayed below your pathway listing all the possible shortest paths. To visualize those paths in your My Pathway, select them by putting a check in the check box and clicking "Add to Pathway".

First click on the Build button:

From the Build button menu, click on the following option:

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Events

 

  

Ingenuity Hosts U.S. User Group Meeting

On June 4-5, 2007, IPA users gathered in San Francisco to network with colleagues, speakers, and Ingenuity's developers to exchange ideas and learn how other scientists use IPA. Attendees also had an opportunity to meet with some of Ingenuity's partners to hear how IPA is integrated with systems such as Affymetrix, Agilent Technologies - GeneSpring, Asuragen, Compendia Bioscience, InforSense, SAS - JMP, and Spotfire.

The most popular aspect of the Users Group Meeting was the workshops on Monday morning. Five interactive workshops (Biomarkers, Chemicals/Metabolites, Core Analysis and Getting Started, Molecular Toxicology, and Search and Explore) were run concurrently. During the morning break, users were tested on their IPA knowledge with a "pop" quiz with prizes for the correct answer. Once again, users had the opportunity to list and vote for features that they would like to see in subsequent releases of IPA. Voting is always exciting and it is interesting to see what attracts the most attention. There definitely was a theme to the feature requests for filtering capabilities for Core/Tox/Biomarker Analyses; tools for modifying networks and pathways; options for network generation; and, enhanced sharing information with colleagues and collaborators.

Networking and socializing with our users is important too. Guests were transported to San Francisco's historic Ferry Building for a wine tasting and food pairing at the Wine Merchant. A very special evening was enjoyed by all the participants.

Megan Laurance, Ph.D., scientist, product marketing, Ingenuity Systems, and Ramon Felciano, Ph.D., Founder, CTO and VP Research, Ingenuity Systems Ingenuity Systems U.S. User Group Meeting, June 4-5, 2007 Ingenuity Systems U.S. User Group Meeting, June 4-5, 2007

Keep checking the Ingenuity Insider for information on the 2008 User Group Meetings tentatively scheduled for early April in Boston and late April in Europe.

Contact Us:

Your comments and suggestions are important. Contact us at 1-800-381-5111 or email support@ingenuity.com.

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Copyright 2007 Ingenuity Systems
www.ingenuity.com | North American Sales: (1) 650.381.5056 | European Sales: +49 173.9076521