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Full-Text Articles in Life Sciences
Estimation And Testing Of Gene Expression Heterosis, Tieming Ji, Peng Liu, Dan Nettleton
Estimation And Testing Of Gene Expression Heterosis, Tieming Ji, Peng Liu, Dan Nettleton
Dan Nettleton
Heterosis, also known as the hybrid vigor, occurs when the mean phenotype of hybrid offspring is superior to that of its two inbred parents. The heterosis phenomenon is extensively utilized in agriculture though the molecular basis is still unknown. In an effort to understand phenotypic heterosis at the molecular level, researchers have begun to compare expression levels of thousands of genes between parental inbred lines and their hybrid offspring to search for evidence of gene expression heterosis. Standard statistical approaches for separately analyzing expression data for each gene can produce biased and highly variable estimates and unreliable tests of heterosis. …
Computational Integration Of Structural And Functional Genomics Data Across Species To Develop Information On The Porcine Inflammatory Gene Regulatory Pathway, C. K. Tuggle, Y. F. Wang, O. P. Couture, L. Qu, J. J. Uthe, D. Kuhar, J. K. Lunney, D. Nettleton, J. C. Dekkers, S. M. D. Bearson
Computational Integration Of Structural And Functional Genomics Data Across Species To Develop Information On The Porcine Inflammatory Gene Regulatory Pathway, C. K. Tuggle, Y. F. Wang, O. P. Couture, L. Qu, J. J. Uthe, D. Kuhar, J. K. Lunney, D. Nettleton, J. C. Dekkers, S. M. D. Bearson
Dan Nettleton
We are investigating the porcine gut immune response to infection through gene expression profiling. Porcine Affymetrix GeneChip data was obtained from RNA prepared from mesenteric lymph node of swine infected with either Salmonella enterica serovar Typhimurium (ST) or S. Choleraesuis (SC) for 0, 8, 24, 48 or 504 hours post-inoculation (hpi). In total, 2,365 genes with statistical evidence for differential expression (DE; p < 0.01, q < 0.26, fold-change> 2) between at least two time-points were identified. Comparative Gene Ontology analyses revealed that a high proportion of annotated DE genes in both infections are involved in immune and defence responses. Hierarchical clustering of expression patterns and …
Spotted Cotton Oligonucleotide Microarrays For Gene Expression Analysis, Joshua A. Udall, Lex E. Flagel, Foo Cheung, Andrew W. Woodard, Ran Hovav, Ryan Adam Rapp, Jordan M. Swanson, Jinsuk J. Lee, Alan R. Gingle, Dan Nettleton, Christopher D. Town, Z. Jeffrey Chen, Jonathan F. Wendel
Spotted Cotton Oligonucleotide Microarrays For Gene Expression Analysis, Joshua A. Udall, Lex E. Flagel, Foo Cheung, Andrew W. Woodard, Ran Hovav, Ryan Adam Rapp, Jordan M. Swanson, Jinsuk J. Lee, Alan R. Gingle, Dan Nettleton, Christopher D. Town, Z. Jeffrey Chen, Jonathan F. Wendel
Dan Nettleton
Microarrays offer a powerful tool for diverse applications plant biology and crop improvement. Recently, two comprehensive assemblies of cotton ESTs were constructed based on three Gossypium species. Using these assemblies as templates, we describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species. Synthetic oligonucleotide probes were generated from exemplar sequences of a global assembly of 211,397 cotton ESTs derived from >50 different cDNA libraries representing many different tissue types and tissue treatments. A total of 22,787 oligonucleotide probes are included on the arrays, optimized to target the …