GeneNet Engine

GeneNet Engine is an exploratory tool to aid hypothesis and biomarker development at a systems-level for genotype-phenotype relationships. Expressed phenotypes may arise due to interactions between multiple genes in a system and effects from the surrounding environment. Therefore, a high systems-level view is needed to identify gene sets causal for a trait. The ability to predict genes that effect important traits is of great importance to agriculture and health. System biology approaches, that combine genomics, gene co-expression networks and data from genetic studies help provide a view at the systems-level of gene interactions. As co-expressed genes tend to be involved in similar processes, it is expected that co-expressed genes may work together to give rise to specific pheontypes. The network module serves as the basic unit of exploration in this site.

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Publications

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A systems-genetics approach and data mining tool to assist in the discovery of genes underlying complex traits in Oryza sativa
PMID: 23874666

metasource: Fairsharing.org
version: None

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• A systems-genetics approach and data mining tool to assist in the discovery of genes underlying complex traits in Oryza sativa PubMed citations: 13.

  13 articles citing: A systems-genetics approach and data mining tool to assist in the discovery of genes underlying complex traits in Oryza sativa

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  Addressing noise in co-expression network construction. PMID:34850822

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  Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases. PMID:34251419

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  Agro-Physiologic Responses and Stress-Related Gene Expression of Four Doubled Haploid Wheat Lines under Salinity Stress Conditions. PMID:33466713

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  Exploration into biomarker potential of region-specific brain gene co-expression networks. PMID:33051491

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  Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases. PMID:31725859

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  Rice Genome-Scale Network Integration Reveals Transcriptional Regulators of Grass Cell Wall Synthesis. PMID:31681374

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  The Plant-Transpiration Response to Vapor Pressure Deficit (VPD) in Durum Wheat Is Associated With Differential Yield Performance and Specific Expression of Genes Involved in Primary Metabolism and Water Transport. PMID:30697225

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  Sorting Five Human Tumor Types Reveals Specific Biomarkers and Background Classification Genes. PMID:29802335

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  Discovering Condition-Specific Gene Co-Expression Patterns Using Gaussian Mixture Models: A Cancer Case Study. PMID:28819158

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  ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data. PMID:28222698

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  blend4php: a PHP API for galaxy. PMID:28077564

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  Designing climate-resilient rice with ideal grain quality suited for high-temperature stress. PMID:25662847

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  Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases. PMID:24163125

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biomarker

metasource: Fairsharing.org
version: None

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co-expression

metasource: Fairsharing.org
version: None

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genotype

metasource: Fairsharing.org
version: None

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network model

metasource: Fairsharing.org
version: None

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phenotype

metasource: Fairsharing.org
version: None

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biomarker co-expression genotype network model phenotype