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Relationship Network Search Engine

JIB-2042

APPLICATIONS OF TECHNOLOGY:

  • Target and lead identification in drug discovery
  • Discovery of additional indications for existing therapeutics
  • Identification of novel interactions in genetic signaling pathways

ADVANTAGES:

  • Accelerates analysis of functional relationships among genes, drugs, and diseases
  • Data on therapeutic drugs can be mined to uncover new modes of action
  • Creates easy to use visual diagrams
  • Compatible with proprietary data sets

ABSTRACT:

GenoPharm is software developed by Kasian Franks and colleagues at Berkeley Lab that facilitates the analysis of complex genetic pathways. GenoPharm uncovers unknown functional relationship networks among genes, drugs, and diseases, and ultimately yields novel target genes and associated lead drug compounds. By bridging the gap between the way machines and humans process information, GenoPharm accelerates research and increases opportunities for discovery.

This screen shot of GenoPharm displays a relationship network among several drugs and related genes. For a larger image, click here.

To use GenoPharm, the user first selects and enters gene symbols, IDs, or keywords. Next, the user chooses a context such as “molecular function” or “therapeutics.” GenoPharm is then ordered to search. The results are displayed as relationship networks. The strength of each relationship is indicated by the distance between each entity, and previously unknown relationship networks are clearly indicated. The most relevant evidence (e.g. PubMed or OMIM reference) connecting the genes is either shown or displayed as a link. GenoPharm allows the user to compare results and zoom in and out to better understand a given relationship network.

GenoPharm adds another dimension to current methods by looking for indirect relationships between genes. For example, two genes can be linked by virtue of the relationship they share with another gene or drug. GenoPharm can filter these relationships further by grouping genes according to their physical location within the cell. These features are anticipated to be of great value in analyzing microarray data.

Berkeley Lab’s Geneva Development System, the engine behind GenoPharm, has been used to process and mine the vast amount of data contained in public biomedical databases, including PubMed, OMIM, and PharmaGKB, as well as data in proprietary databases. The Geneva Development System can also be used to improve the contextual relevancy of networked connections managed by any machine capable of processing information including search and visualization engines.

Requirements:
Server component runs on Linux. Client component accessible through any web browser that supports the Java plugin 1.4.x

STATUS:

Available for licensing or collaborative research.

REFERENCE NUMBER: JIB-2042

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Last updated: 08/17/2010