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Physical Sciences and Mathematics Commons™
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Full-Text Articles in Physical Sciences and Mathematics
The Nuances Of Statistically Analyzing Next-Generation Sequencing Data, Sanvesh Srivastava, R. W. Doerge
The Nuances Of Statistically Analyzing Next-Generation Sequencing Data, Sanvesh Srivastava, R. W. Doerge
Conference on Applied Statistics in Agriculture
High-throughput sequencing technologies, in particular next-generation sequencing (NGS) technologies, have emerged as the preferred approach for exploring both gene function and pathway organization. Data from NGS technologies pose new computational and statistical challenges because of their massive size, limited replicate information, large number of genes (high-dimensionality), and discrete form. They are more complex than data from previous high-throughput technologies such as microarrays. In this work we focus on the statistical issues in analyzing and modeling NGS data for selecting genes suitable for further exploration and present a brief review of the relevant statistical methods. We discuss visualization methods to assess …
Dynamic Clustering Of Cell-Cycle Microarray Data, Lingling An, R. W. Doerge
Dynamic Clustering Of Cell-Cycle Microarray Data, Lingling An, R. W. Doerge
Conference on Applied Statistics in Agriculture
The cell cycle is a crucial series of events that are repeated over time, allowing the cell to grow, duplicate, and split. Cell-cycle systems play an important role in cancer and other biological processes. Using gene expression data gained from microarray technology it is possible to group or cluster genes that are involved in the cell-cycle for the purpose of exploring their functional co-regulation. Typically, the goal of clustering methods as applied to gene expression data is to place genes with similar expression patterns or profiles into the same group or cluster for the purpose of inferring the function of …
Clustering A Series Of Replicated Polyploid Gene Expression Experiments In Maize, Lingling An, Nicole C. Riddle, James A. Birchler, R. W. Doerge
Clustering A Series Of Replicated Polyploid Gene Expression Experiments In Maize, Lingling An, Nicole C. Riddle, James A. Birchler, R. W. Doerge
Conference on Applied Statistics in Agriculture
Ploidy level is defined as the number of individual sets of chromosomes contained in a single cell. Many important crop plants, such as potato, soybean and wheat are polyploid. Although it is widely known that polyploidy is a frequent evolutionary event, it is not fully understand why polyploids have been so successful. In this work cluster analysis is employed to study gene expression changes in a maize inbred line (B73) across a range of polyploidy levels. The B73 ploidy series includes monoploid, diploid, triploid and tetraploid plants and consists of biological and technical replicates as measured by microarray technology. An …