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Full-Text Articles in Life Sciences
Hierarchical Modeling And Differential Expression Analysis For Rna-Seq Experiments With Inbred And Hybrid Genotypes, Andrew Lithio, Dan Nettleton
Hierarchical Modeling And Differential Expression Analysis For Rna-Seq Experiments With Inbred And Hybrid Genotypes, Andrew Lithio, Dan Nettleton
Dan Nettleton
The performance of inbred and hybrid genotypes is of interest in plant breeding and genetics. High-throughput sequencing of RNA (RNA-seq) has proven to be a useful tool in the study of the molecular genetic responses of inbreds and hybrids to environmental stresses. Commonly used experimental designs and sequencing methods lead to complex data structures that require careful attention in data analysis. We demonstrate an analysis of RNA-seq data from a split-plot design involving drought stress applied to two inbred genotypes and two hybrids formed by crosses between the inbreds. Our generalized linear modeling strategy incorporates random effects for whole-plot experimental …
Clustering With Exclusion Zones: Genomic Applications, Mark Segal, Yuanyuan Xiao, Fred Huffer
Clustering With Exclusion Zones: Genomic Applications, Mark Segal, Yuanyuan Xiao, Fred Huffer
Mark R Segal
Methods for formally evaluating the clustering of events in space or time, notably the scan statistic, have been richly developed and widely applied. In order to utilize the scan statistic and related approaches, it is necessary to know the extent of the spatial or temporal domains wherein the events arise. Implicit in their usage is that these domains have no “holes”—hereafter “exclusion zones”—regions in which events a priori cannot occur. However, in many contexts, this requirement is not met. When the exclusion zones are known, it is straightforward to correct the scan statistic for their occurrence by simply adjusting the …
Intracellular Coexpression Of Epidermal Growth Factor Receptor, Her-2/Neu, And P21ras In Human Breast Cancers: Evidence For The Existence Of Distinctive Patterns Of Genetic Evolution That Are Common To Tumors From Different Patients, Stanley E. Shackney, Agnese A. Pollice, Charles A. Smith, Laura E. Janocko, Lillian Sweeney, Kathryn A. Brown, Sarita G. Singh, Lingping Gu, Robert Yakulis, Joseph F. Lucke
Intracellular Coexpression Of Epidermal Growth Factor Receptor, Her-2/Neu, And P21ras In Human Breast Cancers: Evidence For The Existence Of Distinctive Patterns Of Genetic Evolution That Are Common To Tumors From Different Patients, Stanley E. Shackney, Agnese A. Pollice, Charles A. Smith, Laura E. Janocko, Lillian Sweeney, Kathryn A. Brown, Sarita G. Singh, Lingping Gu, Robert Yakulis, Joseph F. Lucke
Joseph Lucke
Multiparameter flow cytometry studies were performed on cells from the primary tumors of 94 patients with breast cancer. Correlated cellular measurements of cell DNA content, Her-2/neu, epidermal growth factor receptor (EGFR), and p21ras levels were performed on each of 5,000 to 100,000 cells from each tumor. When criteria for positivity were matched with those in common use for immunohistochemical studies, 28 of 94 (30\%) breast cancers were classified as positive for Her-2/neu overexpression. When similar criteria were applied to the EGFR measurements, 23 of 94 (24\%) cases were classified as positive for EGFR overexpression. Similarly, 23 of 94 (24\%) cases …
Assessing Sequential Oncogene Amplification In Human Breast Cancer, Laura E. Janocko, Joseph F. Lucke, David W. Groft, Kathryn A. Brown, Charles A. Smith, Agnese A. Pollice, Sarita G. Singh, Robert Yakulis, Robert J. Hartsock, Stanley E. Shackney
Assessing Sequential Oncogene Amplification In Human Breast Cancer, Laura E. Janocko, Joseph F. Lucke, David W. Groft, Kathryn A. Brown, Charles A. Smith, Agnese A. Pollice, Sarita G. Singh, Robert Yakulis, Robert J. Hartsock, Stanley E. Shackney
Joseph Lucke
Studies of amplification and/or overexpression of c-myc, HER-2/neu, and H-ras in breast cancer have shown that each is associated with a poor prognosis. The purpose of this study was to explore the possibility that there is a preferred sequence of amplification of these oncogenes in breast cancer. The frequencies of amplification and patterns of co-amplification of c-myc, HER-2/neu, and H-ras were studied in a group of 84 breast cancers. The data suggested a preferred sequence of amplification that consisted of c-myc amplification-HER-2/neu amplification-H-ras amplification. This model was supported by loglinear analysis. In addition, the levels of amplification of JC-A, a …