Abstract

The main goal of this project is to develop methods of analysis and software implementations for gene expression data, proteomics data, and metabolomics data that are informed by research on the statistical characteristics of the data that are to be analyzed. The principles guiding this methods-development project include the following: 1) high-throughput assay data require transformation so that measurements can be treated in the same fashion across the full range; 2) linear statistical models provide a powerful class of methods that are often sufficient to address the real biological problems at issue (though nonlinear models should be available when required); 3) statistical tests should use appropriate comparison standards so that the tests achieve the highest power consistent with preventing excessive false positives. Under this proposal, we will continue the development of methods and software for gene expression data, and carry over the methods to the analysis of proteomics and metabolomics data by mass spectrometry and NMR spectroscopy. ? ? ?

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Research Project (R01)
Project #
5R01HG003352-03
Application #
7392384
Study Section
Biodata Management and Analysis Study Section (BDMA)
Program Officer
Good, Peter J
Project Start
2006-06-01
Project End
2011-03-31
Budget Start
2008-04-01
Budget End
2011-03-31
Support Year
3
Fiscal Year
2008
Total Cost
$214,323
Indirect Cost

  Institution

Name
University of California Davis
Department
Miscellaneous
Type
Schools of Engineering
DUNS #
047120084
City
Davis
State
CA
Country
United States
Zip Code
95618

  Publications

Oskarsson, Björn; Rocke, David M; Dengel, Karsten et al. (2016) Myasthenia gravis exacerbation after discontinuing mycophenolate: A single-center cohort study. Neurology 86:1159-63
Xia, Jing; Rocke, David M; Perry, George et al. (2014) Differential network analyses of Alzheimer's disease identify early events in Alzheimer's disease pathology. Int J Alzheimers Dis 2014:721453
Stewart, Daniel N; Lango, Jozsef; Nambiar, Krishnan P et al. (2013) Carbon turnover in the water-soluble protein of the adult human lens. Mol Vis 19:463-75
Yunis, Reem; Albrecht, Huguette; Kalanetra, Karen M et al. (2012) Genomic characterization of a three-dimensional skin model following exposure to ionizing radiation. J Radiat Res 53:860-75
Ray, Monika; Yunis, Reem; Chen, Xiucui et al. (2012) Comparison of low and high dose ionising radiation using topological analysis of gene coexpression networks. BMC Genomics 13:190
Barkauskas, Donald A; Rocke, David M (2010) A general-purpose baseline estimation algorithm for spectroscopic data. Anal Chim Acta 657:191-7
Maron, Jill L; Johnson, Kirby L; Rocke, David M et al. (2010) Neonatal salivary analysis reveals global developmental gene expression changes in the premature infant. Clin Chem 56:409-16
Kaplan, Frederick S; Zasloff, Michael A; Kitterman, Joseph A et al. (2010) Early mortality and cardiorespiratory failure in patients with fibrodysplasia ossificans progressiva. J Bone Joint Surg Am 92:686-91
Chen, Ying; Wu, Rebekah; Felton, James et al. (2010) A Method to Detect Differential Gene expression in Cross-Species Hybridization Experiments at Gene and Probe Level. Biomed Inform Insights 2010:1-10
Barkauskas, Donald A; An, Hyun Joo; Kronewitter, Scott R et al. (2009) Detecting glycan cancer biomarkers in serum samples using MALDI FT-ICR mass spectrometry data. Bioinformatics 25:251-7

Showing the most recent 10 out of 22 publications