Publication Focus: Reproductive Health and Disorders

As part of an ongoing strategy to address unmet needs in the field of reproductive health, researchers are taking genomic and proteomic approaches to understand the etiology of reproductive system disorders with an aim of developing novel therapeutic interventions and more effective diagnostic markers of disease. In the past year, there has been a surge in publications in which researchers use IPA in order to identify mechanisms of female and male fertility, molecular signatures of fertile oocytes, create models for the pathology of endometriosis, unravel the complex mechanisms controlling preimplantation development, mammary development during pregnancy and lactation, and onset of labor.

Below we’ve highlighted a sample of some of the more recent IPA publications in this area. For a complete list of Reproductive Health publications citing IPA, please go to http://www.ingenuity.com/library/search-pub.html, and select “Reproductive Biology” from the “Research Area/Field of Interest” search field.

• Comprehensive proteomic analysis of bovine spermatozoa of varying fertility rates and identification of biomarkers associated with fertility.
  BMC Syst Biol. 2008 Feb 22;2(1):19 [Epub ahead of print] Peddinti D, Nanduri B, Kaya A, Feugang JM, Burgess SC, Memili E.
• Gene regulatory networks in lactation: identification of global principles using bioinformatics.
  BMC Syst Biol. 2007 Nov 27;1(1):56 [Epub ahead of print] Lemay DG, Neville MC, Rudolph MC, Pollard KS, German JB.
• Oxidative Stress, Gene Expression, and Protein Changes Induced in the Human Placenta during Labor.
  Am J Pathol. 2007 Oct;171(4):1168-79. Epub 2007 Sep 6. Cindrova-Davies T, Yung HW, Johns J, Spasic-Boskovic O, Korolchuk S, Jauniaux E, Burton GJ, Charnock-Jones DS.
• Human endometriosis is associated with plasma cells and overexpression of B lymphocyte stimulator.
  Proc Natl Acad Sci U S A. 2007 Jul 24;104(30):12451-6. Epub 2007 Jul 17. Hever A, Roth RB, Hevezi P, Marin ME, Acosta JA, Acosta H, Rojas J, Herrera R, Grigoriadis D, White E, Conlon PJ, Maki RA, Zlotnik A.
• Labor-Associated Gene Expression in the Human Uterine Fundus,Lower Segment,and Cervix.
  PLoS Med. 2006 Jun;3(6): e169. Epub 2006 Jun 13. Bukowski R,Hankins GD,Saade GR,Anderson GD,Thornton S.

Product Updates

Ingenuity has another content release in September. This release highlights a number of important content areas including:

• Gene-to-Disease Associations: Thousands of new gene-to disease associations from OMIM for hundreds of genetic disorders allow you to discover a wider spectrum of diseases related to your genes of interest.
• Protein Ubiquitination Content: New manually curated protein ubiquitination content allows you to gain a better understanding of molecular mechanisms of protein stability and degradation
• New Immunology Pathways: Eleven new immunology-related pathways and enhanced precision in immunology findings help you find the immunology information you are looking for.
• Host-Pathogen Interactions: Additional interactions and regulatory events between pathogen and host proteins have been added.
• Women’s Health Content: Additional content to understand the etiology of reproductive system disorders supports the development of novel therapeutic interventions and the discovery of more effective diagnostic markers of disease.
• Additional Clinical Trial Information: You can now see what drugs are in trial for various indications and see what other companies are working on, to help with ideas for next-generation drugs and with prioritization of existing projects.

  Learn more

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PDF Resources to Download

We have created a number of whitepapers to provide tangible examples of how IPA can be used to address a variety of research challenges. These whitepapers focus on features that are having a significant impact on life scientists’ workflows and experiences with IPA, and we have created these whitepapers to provide clear, concise information on how and when to apply these features to your own research. Click on the below links to download these valuable resources about IPA.

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Quick Tip: How can I find which genes in a molecule’s neighborhood are specific to my dataset?

Click Apply when finished. Then use the Autolayout button to space the molecules appropriately.

The molecules will be colored as they are expressed in your analysis. Red indicates up-regulation. Green indicates down-regulation. Gray indicates that the molecule was measured but did not meet your cutoff value.

Questions on this tip? Give us a call at 650.381.5111, or email support@ingenuity.com.

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Feature Highlight: Shared Folder Email Option

For those of you who frequently collaborate with the same people on projects, the Share Manager in IPA now simplifies the task by storing previously used email addresses for easy access. This enables you to quickly choose from a list of people you share your data with regularly, and share pathways and analysis with them along with a customized message.

The Share Manager can be accessed from the File menu, Share, Share Manager. Click on "Add" next to the Shared Project Members box. New email addresses can be added in the "Add new email(s)" tab. Existing emails can be selected and added to the project by clicking "Add".

Currently there is no limit on the number of email addresses that can be stored in your IPA account. Questions on this feature? Give us a call at 650.581.3111 or email support@ingenuity.com.

Ingenuity News

We've had an exciting few months, as Ingenuity has broadened its business offerings and expanded into more services and strategic partnerships.

Check out what the press had to say about us in the last few months:

Bioinform recently explored the new ways that IPA is being used as a knowledge management platform for disease-specific research by CHDI, an organization focused on Huntington’s disease. Ingenuity is also doing custom, disease-specific knowledge curation for CHDI. IPA was selected by CHDI after a year of evaluation, because of the unique and user-friendly way that IPA can structure and integrate biological information currently located in multiple databases.

  Continue reading the article at: http://www.bioinform.com/issues/12_29/features/148282-1.html.

Drug Discovery and Development recently published an article titled “Building Bundles of Biomarkers”, which discussed how IPA can be used for biomarker validation by filtering a list of biomarkers down to the most relevant ones, based on parameters such expression level, tissue distribution, disease association, and more – all linked directly to the supporting literature.

  Continue reading the article at: http://www.dddmag.com/Article-Identifying-and-Validating-Biomarkers.aspx.

New: Ingenuity Analysis Services – We’ve just launched our new scientific services offering, designed to help you maximize research efficiency and help teams that need rapid turnaround or who don't have in-house resources.

We can help with:

• Analysis and interpretation of 'omics datasets for compound profiling, lead identification and prioritization of therapeutic targets, and understanding disease mechanism of action and mechanism of toxicity.
• Building biological models of disease processes for target identification and validation research.
• Identification and prioritization of biomarkers via analysis of gene expression array, proteomics, or genotyping data.
• Delivering a focused toxicity and safety assessment of drug candidates.
• Creating clear report summaries and graphics or pathways for presentations, publications, or easy collaboration.

  Download the fact sheet here

For more information, contact analytics@ingenuity.com, or call 650.381.5111.

Events

We take pride in providing training and support to customers in the pharma, biotech, academic, government, and farm settings. At the NCI-Frederick/ Ft. Dietrich Research Festival (above), the hay added to the festive barnyard décor. We enjoyed meeting you there and answering your questions about IPA.

Visit us next at:

• 2008 Biomedical Research Equipment and Supplies Exhibit
  (at Harvard Medical School)
  September 24-25, 2008 Boston, MA
  
  
• CHI Biomarker Discovery Summit
  Sept 29-Oct 1, Philadelphia, PA
  Booth 15
  Ingenuity Presentation - Sept 30 at 9:25am

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We're hiring!

Do you know someone who would be interested?

Our technologies help life science researchers more effectively search, explore, visualize, and analyze biological and chemical findings related to genes, proteins, and small molecules (e.g. drugs). Our solutions are created by biologists and developers who combine innovative semantic search, ontology, and software development technologies with life science research expertise. Some current positions include:

• Academic Sales Rep – Eastern Region
• Bioinformatics Engineer
• Consulting Ontologist
• Content QA Software Engineer
• Field Application Scientist – Asia Pacific
• Key Account Sales Rep – Europe

» Click here to browse all of our current openings

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