Open Access. Powered by Scholars. Published by Universities.®

Life Sciences Commons

Open Access. Powered by Scholars. Published by Universities.®

2006

Genetics and Genomics

Statistics Publications

Articles 1 - 4 of 4

Full-Text Articles in Life Sciences

Estimating The Number Of True Null Hypotheses From A Histogram Of P Values, Dan Nettleton, J.T. Gene Hwang, Rico A. Caldo, Roger P. Wise Sep 2006

Estimating The Number Of True Null Hypotheses From A Histogram Of P Values, Dan Nettleton, J.T. Gene Hwang, Rico A. Caldo, Roger P. Wise

Statistics Publications

In an earlier article, an intuitively appealing method for estimating the number of true null hypotheses in a multiple test situation was proposed. That article presented an iterative algorithm that relies on a histogram of observed p values to obtain the estimator. We characterize the limit of that iterative algorithm and show that the estimator can be computed directly without iteration. We compare the performance of the histogram-based estimator with other procedures for estimating the number of true null hypotheses from a collection of observed p values and find that the histogram-based estimator performs well in settings similar to those ...


Scanning Microarrays At Multiple Intensities Enhances Discovery Of Differentially Expressed Genes, David S. Skibbe, Xiujuan Wang, Xuefeng Zhao, Lisa A. Borsuk, Dan Nettleton, Patrick S. Schnable Aug 2006

Scanning Microarrays At Multiple Intensities Enhances Discovery Of Differentially Expressed Genes, David S. Skibbe, Xiujuan Wang, Xuefeng Zhao, Lisa A. Borsuk, Dan Nettleton, Patrick S. Schnable

Statistics Publications

Motivation: Scanning parameters are often overlooked when optimizing microarray experiments. A scanning approach that extends the dynamic data range by acquiring multiple scans of different intensities has been developed.

Results: Data from each of three scan intensities (low, medium, high) were analyzed separately using multiple scan and linear regression approaches to identify and compare the sets of genes that exhibit statistically significant differential expression. In the multiple scan approach only one-third of the differentially expressed genes were shared among the three intensities, and each scan intensity identified unique sets of differentially expressed genes. The set of differentially expressed genes from ...


Gene Expression Profiling In Salmonella Choleraesuis-Infected Porcine Lung Using A Long Oligonucleotide Microarray, Shu-Hong Zhao, Daniel Kuhar, Joan K. Lunney, Harry Dawson, Catherine Guidry, Jolita J. Uthe, Shawn M. D. Bearson, Justin Recknor, Dan Nettleton, Christopher K. Tuggle Jul 2006

Gene Expression Profiling In Salmonella Choleraesuis-Infected Porcine Lung Using A Long Oligonucleotide Microarray, Shu-Hong Zhao, Daniel Kuhar, Joan K. Lunney, Harry Dawson, Catherine Guidry, Jolita J. Uthe, Shawn M. D. Bearson, Justin Recknor, Dan Nettleton, Christopher K. Tuggle

Statistics Publications

Understanding the transcriptional response to pathogenic bacterial infection within food animals is of fundamental and applied interest. To determine the transcriptional response to Salmonella enterica serovar Choleraesuis (SC) infection, a 13,297-oligonucleotide swine array was used to analyze RNA from control, 24-h postinoculation (hpi), and 48-hpi porcine lung tissue from pigs infected with SC. In total, 57 genes showed differential expression (p < 0.001; false discovery rate = 12%). Quantitative real-time PCR (qRT-PCR) of 61 genes was used to confirm the microarray results and to identify pathways responding to infection. Of the 33 genes identified by microarray analysis as differentially expressed, 23 were confirmed by qRT-PCR results. A novel finding was that two transglutaminase family genes (TGM1 and TGM3) showed dramatic increases in expression postinoculation; combined with several other apoptotic genes, they indicated the induction of apoptotic pathways during SC infection. A predominant T helper 1-type immune response occurred during infection, with interferon γ ...


Gene Expression Programs During Shoot, Root, And Callus Development In Arabidopsis Tissue Culture, Ping Che, Sonia Lall, Dan Nettleton, Stephen H. Howell Jun 2006

Gene Expression Programs During Shoot, Root, And Callus Development In Arabidopsis Tissue Culture, Ping Che, Sonia Lall, Dan Nettleton, Stephen H. Howell

Statistics Publications

Shoots can be regenerated from Arabidopsis (Arabidopsis thaliana) root explants in tissue culture through a two-step process requiring preincubation on an auxin-rich callus induction medium. Regenerating tissues can be directed along different developmental pathways leading to the formation of shoots, new roots, or callus by transferring to the appropriate organ induction medium. Using gene-profiling methods, we identified groups of genes that serve as molecular signatures of the different developmental processes, i.e. genes that were specifically up- or down-regulated on one developmental pathway, but not on others. One transcription factor gene that was up-regulated during early shoot development was RAP2 ...