In December, Ingenuity launched the latest release of IPA, featuring contextual data analysis. Contextual data analysis enhances IPA's powerful search and analysis capabilities by enabling researchers to refine their experimental analyses and develop scientific hypothesis based on findings that have been demonstrated to occur in a particular species, cell type, tissue, bio-fluid, biological process, cellular function, chemical, and disease of interest. For example, a CNS researcher can run an analysis and identify molecular interactions and gene-to-phenotype associations that have been demonstrated to occur specifically in CNS tissues or cell lines — thus narrowing the hypothesis space to one closely aligned with their experimental model.

Other new capabilities in IPA 7 are:

• microRNA target information
• New Reporting Tools
• New Signaling Pathways
• Additional Chemical Content

Want all the details about what's new in IPA? Click the button below.

Did you know that IPA now categorizes the Signaling and Metabolic Canonical Pathways? In the Project Manager, expand the Libraries section by clicking on the "+" signs. Each category can be further expanded to view the individual Canonical Pathways. These categories are also present in the Customize Chart menu on the Canonical Pathway bar chart from within an Analysis, so that you can have a broader picture of the mechanisms that are changing within your data. Canonical Pathways may be categorized in more than one place if they participate in more than one function.

Additionally, each Canonical Signaling Pathway also has a corresponding description to provide you with an overview of the pathway. To access the description, select a Canonical Pathway from the Library, then right click and choose "Show Description".

» Back to top

Recent publications in the field of lung disease highlight how IPA is helping researchers better understand the underlying pathophysiology of lung diseases that have high morbidity rates, poor diagnostic tools, and lack of effective treatments – diseases like asthma, mesothelioma and acute respiratory distress syndrome. Through analysis of data from genome wide expression studies, exon arrays, and proteomics platforms, as well as in silico pathway exploration, IPA is enabling researchers to successfully identify novel mediators of disease, validate potential therapeutic targets, and identify better diagnostic and prognostic biomarkers.

Below we've highlighted a sample of some of the more recent IPA publications in the area of lung disease. For complete list of related publications citing IPA, please go to http://www.ingenuity.com/library/search-pub.html, and search with the key word "lung" in the keyword field.

• New asthma biomarkers: lessons from murine models of acute and chronic asthma.
  Am J Physiol Lung Cell Mol Physiol. 2008 Nov 21. [Epub ahead of print] Di Valentin E, Crahay C, Garbacki N, Hennuy B, Gueders M, Noel A, Foidart JM, Grooten J, Colige A, Piette J, Cataldo D.
• Pathway targets to explore in the treatment of non-small cell lung cancer.
  J Thorac Oncol. 2008 Nov;3(11):1342-52. Weiss GJ, Kingsley C.
• Whole genome exon arrays identify differential expression of alternatively spliced, cancer-related genes in lung cancer.
  Nucleic Acids Res. 2008 Oct 16. [Epub ahead of print] Xi L, Feber A, Gupta V, Wu M, Bergemann AD, Landreneau RJ, Litle VR, Pennathur A, Luketich JD, Godfrey TE.
• Novel Functional View of the Crocidolite Asbestos-Treated A549 Human Lung Epithelial Transcriptome Reveals an Intricate Network of Pathways with Opposing Functions.
  BMC Genomics. 2008 Aug 7;9(1):376. [Epub ahead of print] Hevel JM, Olson-Buelow LC, Ganesan B, Stevens JR, Hardman JP, Aust AE.
• Proteomic and computational analysis of bronchoalveolar proteins during the course of the acute respiratory distress syndrome.
  Am J Respir Crit Care Med. 2008 Jul 24. [Epub ahead of print] Chang DW, Hayashi S, Gharib SA, Vaisar T, King ST, Tsuchiya M, Ruzinski JT, Park DR, Matute-Bello G, Wurfel MM, Bumgarner R, Heinecke JW, Martin TR.

» Back to top

Streamline your pathways down to specific and relevant findings.

IPA 7 has implemented a new Species filter where you can limit a My Pathway, Network, Neighborhood, or Canonical Pathway to display molecules and/ or relationships that are specific to one or more species. The Species filter is available from the Build tools (Grow, Path Explorer, Connect, Trim, and Keep) and from the Highlight Tool (found within the Overlay tools). The Species filter also has two associated filters that can be set. The Stringent filter indicates that both the molecules and the relationships must occur in the selected species. The Relaxed filter indicates that only the molecules must occur in the selected species. The Stringent filter is more precise for viewing species-specific information, but may return fewer results.

Problem:

Solution:

1.

We will first apply the Stringent filter. Click on Build to access the Build tools. Choose "Keep" from the pull-down menu.

2.

3.

Expand the Species filter by clicking on the "+" sign. Put a check in the box next to Rat, and put the radio button in the Stringent Filter. These settings indicate that we only wish to keep molecules and relationships that occur in Rat.

5.

Using the Relaxed filter will keep many more of the interactions, because the Relaxed filter only takes into account the species the molecules are expressed in. Relationships can occur in any species or be unspecified.

For more information about how to use the Species filters in IPA, please contact Customer support at support@ingenuity.com or 650-381-5111 (6 am - 5 pm Pacific Time, Monday through Friday).

Sigma Debuts Its "Powered by Ingenuity" Search Functionality

Sigma Aldrich recently launched a new version of it's "Your Favorite Gene" search tool (YFG) that is now powered by Ingenuity technology. YFG Powered by Ingenuity is a free online search tool that helps you quickly locate the products that are most relevant to your research. The new tool integrates Ingenuity's Knowledge Base and search technology with Sigma's life science product portfolio to allow researchers to quickly identify products that are most relevant to the biological and chemical relationships they are examining. » Learn more and check out the Sigma-Aldrich "Your Favorite Gene Search Powered By Ingenuity" » Click here to read the press release

Screenshot of the new YFG Powered by Ingenuity. Genes of interest are placed in a pathway for easy discovery of releated and relevant products.

Scientific Success with Ingenuity

At Ingenuity, we're proud that IPA continues to be a leading tool helping researchers uncover new insights into the molecular basis of disease. In August , we were happy to announce the 1000th publication to cite IPA in its findings.

Want to see how IPA has helped researchers in your field? Check out our searchable publication list at http://www.ingenuity.com/1000_publications/landing.html. (We've recently improved the search capabilities across our bibliography, so even if you've searched before, take another look and see how IPA can help in your area of research.)

Have you published with IPA? Every month we feature a Science Spotlight on our website, highlighting the innovative research that is being conducted using IPA. Think your article could qualify and want to be featured on our homepage? Send an email with information about your publication and how you used IPA to apalmer@ingenuity.com.

IPA 7 Featured in Predictive Biomedicine

In the December 4 issue of the Predictive Biomedicine newsletter, John Russell, editor of Bio-IT World.com, highlighted the new capabilities of IPA 7. Heidi Bullock, Ingenuity's Director of Marketing, told Russell that ""What is unique about IPA's contextual data analysis is the ability to filter not just on your analysis results, but the ability to constrain your hypothesis space upfront – to develop a relevant hypothesis/model from the beginning." According to the article, "Ingenuity says the enhanced functionality will help researchers save time by quickly honing in on the results that are most relevant to their experimental model or experimental conditions." The article also notes the addition of microRNA content and Ingenuity's ongoing commitment to adding disease-specific content to help therapeutic area researchers. Read the full article by clicking here.

Visit Ingenuity at these upcoming conferences in 2009:

• ABRF: February 8-10, Memphis, TN. (Booth 518)
  Ingenuity presentation 2/9 at 6:30 pm.
  
  
• Molecular Medicine: February 24-27, San Francisco, CA. (Booth 301)
  Ingenuity presentation 2/26 at 10:30 am.
  
  
• Biomarkers Congress: February 26-27, Manchester, UK"
  
  
• SOT: March 15-19, Baltimore, MD. (Booth 3016)
  Ingenuity presentation 3/16 at 12:15 pm.

Save the date! Schedule announced for IPA User Group Meetings

This year's User Group Meetings will feature scientific lectures from industry leaders as well as a new optional focused training component. Stay tuned for more information!

• Barcelona, Spain: 4-5 June
• Boston, MA: May 5-6

Start the New Year right — Get IPA Certified

The IPA Certification Program is a free online course offered by Ingenuity Systems for customers who want an in-depth understanding of IPA. This structured curriculum provides comprehensive training in IPA and includes a certification exam. After successfully completing the course and exam, the student receives official certification as an IPA Certified Analyst.

» Learn more about IPA Certification

» Back to top