Abstract

. Decrease the amount of RNA needed. In many cases probe material is limiting the experiments. Smaller sample sizes will allow the study of histological samples and developmental studies. Presently, about 100 microgram of total RNA is required to day a micro-array experiments. Optimizing the hybridization process will substantially reduce the sample size. A calculation indicates that currently only a small percentage (less than 1%) of transcripts even have an opportunity to hybridize to their target. This could be increased to close to 100% by efficient mixing and reducing the total area of the micro-array. . Increase the reliability of measurements. Typically, micro-array experiments are compared to a control. The two are simultaneously hybridized to the micro-array, but labeled with different color fluorophores. Results are expressed as a ratio of the two measurements. When a gene is rarely expressed in the control, the ratio is often unreliable. By building a three color scanner, and using genomic DNA as an internal control, I will be able to make an independent measurement of the DNA content of each spot in the micro-array. This will allow cross- comparison of measurements over time and between laboratories. . Provide new tools to interpret the data. A single experiment can easily generate data on 5,000-40,000 different genes. Software is needed to provide an interface to the wealth of data collected. New methods of analysis must be developed to make sense of the data.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Career Transition Award (K22)
Project #
5K22HG000047-05
Application #
6835068
Study Section
Ethical, Legal, Social Implications Review Committee (GNOM)
Program Officer
Graham, Bettie
Project Start
2000-02-11
Project End
2006-05-31
Budget Start
2004-01-01
Budget End
2006-05-31
Support Year
5
Fiscal Year
2004
Total Cost
$241,787
Indirect Cost

  Institution

Name
University of California Irvine
Department
Engineering (All Types)
Type
Schools of Engineering
DUNS #
046705849
City
Irvine
State
CA
Country
United States
Zip Code
92697

  Publications

Mao, Grace; Brody, James P (2007) Dynamic SPR monitoring of yeast nuclear protein binding to a cis-regulatory element. Biochem Biophys Res Commun 363:153-8
Thompson, H Garrett R; Harris, Joseph W; Brody, James P (2004) Post-translationally modified S12, absent in transformed breast epithelial cells, is not associated with the 26S proteasome and is induced by proteasome inhibitor. Int J Cancer 111:338-47
Thompson, H Garrett R; Harris, Joseph W; Lin, Limin et al. (2004) Identification of the protein Zibra, its genomic organization, regulation, and expression in breast cancer cells. Exp Cell Res 295:448-59
Lin, Limin; Harris, Joseph W; Thompson, H Garrett R et al. (2004) Surface plasmon resonance-based sensors to identify cis-regulatory elements. Anal Chem 76:6555-9
Thompson, H Garrett R; Harris, Joseph W; Wold, Barbara J et al. (2003) p62 overexpression in breast tumors and regulation by prostate-derived Ets factor in breast cancer cells. Oncogene 22:2322-33
Thompson, H Garrett R; Harris, Joseph W; Wold, Barbara J et al. (2002) Identification and confirmation of a module of coexpressed genes. Genome Res 12:1517-22
Brody, James P; Williams, Brian A; Wold, Barbara J et al. (2002) Significance and statistical errors in the analysis of DNA microarray data. Proc Natl Acad Sci U S A 99:12975-8