MetaMiner™ Cystic Fibrosis (MMCF) represents a version of GeneGo’s MetaDiscovery™ suite that is enriched with content specific for cystic fibrosis. It is an ongoing project that was initiated in 2007 by GeneGo Inc. in collaboration with Cystic Fibrosis Foundation Therapeutics (CFFT) and a committee of expert scientists. This reiterative process is mediated and fully funded by CFFT allowing GeneGo developers to maintain and update CF content under the guidance of the Committee*.

Now in its second phase of development, the content is rich in cause-effect relationships including: gene-disease, compounds-disease and compound-protein associations. Therefore, MMCF is a data analysis platform designed to be used by a broad range of CF researchers including wet lab biologists, bioinformaticians, toxicologists, clinicians and chemists.

Figure Legend - MetaCore‘s “Enrichment Analysis” workflow was used to determine representative functions of 2 cystic fibrosis data sets (protein expression from HEK293 cells expressing wild-type or DF508 CFTR ref: PMID: 17110338). Below is one of the most .enriched maps. from the GeneGo Maps ontology (Regulation of degradation of deltaF508 CFTR in CF) with the data overlaid. The pre-built interactive maps are useful hypothesis-driving tools complete with cause-effect relationships marked with directionality (arrows) and mechanisms with links to the literature (hexagons), and the ability to overlay the input data (represented by red bars). In this example bar #1 = HEK cells expressing wild-type CFTR and #2 = HEK cells expressing the mutant. On disease-specific maps such as this one, disease-specific augmented interactions are marked by magenta-colored arrows and text boxes.

The latest MMCF annotation update includes the following:

1. A one-stop shop “Disease Detail” page summarizing all MMCF information.
2. 206 disease-relevant genes
3. 42,173 physical and functional interactions with other human proteins, DNA, RNA and compounds.
4. 12 CF-specific biomarkers (7 metabolites and 5 proteins) with a total of 457 association links
5. Diversified annotation of gene -> disease association according to the following categories
   • Promoter methylation
   • Rearrangement
   • Point mutation
   • Single nucleotide polymorphism (SNP)
   • RNA splice variant
   • RNA amount change
   • Altered interaction
   • Change in Protein Abundance
6. Additional CF Specific Maps for a total of 36 that now include:
   • 10 CFTR traffic and folding related maps
   • 5 different Cholesterol and Sphingolipids transport related to CF
   • 2 different CF-specific immune response maps
   • 4 different Lipoxin maps
   • 2 maps on the influence of Mucin expression
   • 3 maps describing CFTR activation
   • 10 additional maps that describe CFTR in the context of bacterial infection, regulation of ion channels, CFTR translation, and degradation, cytokine production and CFTR gating.
7. 10 CFTR global networks
8. 11 endogenous metabolites annotated for CFTR association
9. 90 drugs and compounds linked to CF (FDA, pre-clinical, clinical trial and discontinued drugs)

For a complete list of MMCF specific maps visit our website at http://www.genego.com/mapbrowse.php?folder=25 and review the list under the “Lung Diseases” folder.

The advanced applications of MMCF also include integration of GeneGo-based analyses with third-party software suites to enable seamless export of networks or analysis lists from MMCF to Cytoscape, GeneSpring, DecisionSite, ArrayStudio and Resolver, following the addition of the appropriate plug-ins.

A sample of how MMCF information can be used with GeneGo‘s MetaDiscovery platform, down load the following white papers here. To access a recorded webinar by Dr. Jerry Wright of an example of how MMCF enhanced his research click here.

For a training session on how to execute these approaches, please contact training@genego.com.

*Cystic Fibrosis Committee Members:

Jerry Wright, Ph.D. Tzyh-Chang Hwang, M.D., Ph.D.
Christopher Karp, M.D. Benjamin Gaston, M.D.
Pamela Zeitlin, MD, Ph.D. Thomas Kelley, Ph.D.
Ann Harris, Ph.D., M.A.
Diana Wetmore, Ph.D. and Elizabeth Joseloff, Ph.D. (CFFT Sponsors)

MetaMiner Cystic Fibrosis is included in MetaCore. If you would like pricing information please contact sales@genego.com or call 1 858 756 7996. For trial access please email trials@genego.com.