By a News Reporter-Staff News Editor at Biotech Business Week -- New research on Data Mining is the subject of a report. According to news reporting from Clemson, South Carolina, by NewsRx journalists, research stated, "Many traits of biological and agronomic significance in plants are controlled in a complex manner where multiple genes and environmental signals affect the expression of the phenotype. In Oryza sativa (rice), thousands of quantitative genetic signals have been mapped to the rice genome."
The news correspondents obtained a quote from the research from Clemson University, "In parallel, thousands of gene expression profiles have been generated across many experimental conditions. Through the discovery of networks with real gene co-expression relationships, it is possible to identify co-localized genetic and gene expression signals that implicate complex genotype-phenotype relationships. In this work, we used a knowledge-independent, systems genetics approach, to discover a high-quality set of co-expression networks, termed Gene Interaction Layers (GILs). Twenty-two GILs were constructed from 1,306 Affymetrix microarray rice expression profiles that were pre-clustered to allow for improved capture of gene co-expression relationships. Functional genomic and genetic data, including over 8,000 QTLs and 766 phenotype-tagged SNPs (p-value less than or equal to0.001) from genome-wide association studies, both covering over 230 different rice traits were integrated with the GILs. An online systems genetics data-mining resource, the GeneNet Engine, was constructed to enable dynamic discovery of gene sets (i.e. network modules) that overlap with genetic traits. GeneNet Engine does not provide the exact set of genes underlying a given complex trait, but through the evidence of gene-marker correspondence, co-expression, and functional enrichment, site visitors can identify genes with potential shared causality for a trait which could then be used for experimental validation. A set of 2 million SNPs was incorporated into the database and serve as a potential set of testable biomarkers for genes in modules that overlap with genetic traits."
According to the news reporters, the research concluded: "Herein, we describe two modules found using GeneNet Engine, one with significant overlap with the trait amylose content and another with significant overlap with blast disease resistance."
For more information on this research see: A systems-genetics approach and data mining tool to assist in the discovery of genes underlying complex traits in Oryza sativa. Plos One, 2013;8(7):e68551. (Public Library of Science - www.plos.org; Plos One - www.plosone.org)
Our news journalists report that additional information may be obtained by contacting S.P. Ficklin, Plant and Environmental Sciences, Clemson University, Clemson, South Carolina, United States (see also Data Mining).
Keywords for this news article include: Clemson, United States, South Carolina, Information Technology, North and Central America, Information and Data Mining.
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