SRI International Demonstrates Computational Method for Mapping and Predicting Human Metabolic Pathways and Proteins
HumanCyc Bioinformatics Database Increases Genomic Collaboration
MENLO PARK, Calif. – February 16, 2005– SRI International, an independent nonprofit research and development organization, has performed a computational analysis of the human genome to predict metabolic pathways and to predict new gene functions within the human genome. Using SRI's PathoLogic(TM) software , the analysis assigned 622 human enzymes to roles in 135 predicted metabolic pathways. The pathways and the analysis results are available in the HumanCyc database.
The HumanCyc database is the seventeenth in SRI's growing collection of BioCyc pathway and genome databases. HumanCyc provides a genome-based view of human nutrition that could foster a better understanding of the links between genome, diet and health.
"The human genome is incredibly vast and complex; Pathways provide a framework for organizing the human genome so that scientists can more easily understand and manipulate it according to the molecular interactions among genes," said Peter Karp, Ph.D., director of SRI's Bioinformatics Research Group. "SRI's goal is to provide biologists with the 'power tools' they need to understand and analyze the genome in a much more useful way. By structuring information into pathways, we provide a unique genomic framework to more easily group and analyze our biochemical machinery. For example, one pathway in the HumanCyc database describes genes that work together to break down nicotine; another pathway contains the group of genes that make cholesterol."
One of SRI's software tools, the HumanCyc Omics Viewer, allows researchers to visualize combinations of gene expression, proteomics, and metabolomics data by painting them onto the cellular overview of human metabolism. This pathway framework also allowed SRI to identify 203 probable missing enzymes in the human genome, and SRI's newly developed pathway hole filling algorithm generated high-scoring candidate genes for 25 of those enzymes.
As part of this work, SRI researchers compared the metabolic pathways of humans and two other well-understood organisms, Escherichia coli (the bacteria better known as E. coli ) and Arabidopsis thaliana, a small flowering plant widely used as a model organism in plant biology. The researchers were able to identify 35 pathways shared among the three organisms: human, bacteria and plant.
For this work, SRI researchers partnered with researchers at Stanford University and Indiana University-Purdue University of Indianapolis. An article about the group's collective findings, "Computational prediction of human metabolic pathways from the complete human genome," was published in the December 22, 2004 issue of Genome Biology.
About HumanCyc
HumanCyc is part of SRI's BioCyc Database Collection, a group of pathway and genome databases that includes EcoCyc, MetaCyc, and databases for 163 other species; the MetaCyc metabolic pathway database contains data from 350 species. Scientists can use BioCyc databases to visualize the layout of genes within a chromosome, a complete biochemical pathway, and the full metabolic map of an organism.
SRI's Pathway software tools combine representation and inference techniques from artificial intelligence with extensive scientific visualization capabilities. The software enables both analysis and web publishing of model-organism databases that integrate genome and pathway information to harness the overwhelming amount of information produced by large-scale genome sequencing efforts.
About SRI's Bioinformatics Research Group
SRI International's Bioinformatics Research Group is a leader in the development of database content and software tools for the bioinformatics field. To date, SRI has licensed Pathway software tools to more than 400 academic and commercial organizations.
About SRI International
Silicon Valley-based SRI International ( www.sri.com ) is one of the world's leading independent research and technology development organizations. Founded as Stanford Research Institute in 1946, SRI has been meeting the strategic needs of clients for almost 60 years. The nonprofit research institute performs client-sponsored research and development for government agencies, commercial businesses and private foundations. In addition to conducting contract R&D, SRI licenses its technologies, forms strategic partnerships and creates spin-off companies.
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