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Bioinformatics Tools for CF

GeneGo 

GeneGo, a Thomson Reuter business, provides systems biology data mining and analysis software tools. The GeneGo’s bioinformatics tool, MetaCore™, is an Oracle-based database derived from input of manually curated primary literature. 

MetaCore™ is designed to identify the underlying biology behind different types of high-throughput experimental data toward assisting with identifying biomarkers for specific disease states, patient profiling in clinical trials, and drug target selection and validation. The visual data maps and networks enable researchers to formulate and test hypotheses.

In 2007, GeneGo, Cystic Fibrosis Foundation Therapeutics (CFFT), and a committee of expert scientists within the CF research community collaborated to develop a CF-specific pathway analysis platform as part of GeneGo’s MetaMiner disease program. MetaMiner™ CF provides knowledge mining and data analysis to a broad range of CF researchers.

To make information more accessible, MetaMiner™ CF provides a database to store CF biological and chemical experimental data in one location. In addition, MetaMiner™ CF displays gene-disease, compounds-disease and compounds-protein relationships.

The content of MetaMiner™ CF was derived from scientific articles and manually curated by the CFFT-GeneGo scientific committee. MetaMiner™ CF is updated on a quarterly basis to reflect recently published CF literature. The visualization tools created by MetaMiner™ CF are intended to help depict key disease-causative and disease progressive mechanisms in a series of pathway maps and network models.

MetaMiner™ CF has created more than 35 maps, covering a range of CF pathways, including those related to:

  • CFTR trafficking and folding 
  • Cholesterol and sphingolipids transport 
  • CF immune response 
  • Mucin expression in CF 
  • CFTR activation 
  • The effects of bacterial infections in CF airways

Researchers can build custom networks of experimental data using GeneGo’s Network Building Algorithms. One of the key benefits of MetaMiner is that it provides direct access to associated literature references with direct links to PubMed. Researchers can browse, access, and export directly to EndNote or Excel information from the database to use in their research.

Using the MetaDiscovery Platform researchers are able to find or produce hypothesis-driven outputs. GeneGo is also the proprietor of MetaDrug™ and ToxHunter™, a complete systems pharmacology platform that is used to predict human metabolites, toxicity and mode of action of novel small molecule compounds.

The map images can be downloaded free of charge, but use of the full MetaMiner™ CF platform capability requires a software subscription. The pathway maps are accessible online on the GeneGo website at www.genego.com.

For more information on MetaMiner™ CF read the white paper.

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