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Overview
The Bioinformatics and Biostatistics Facility Core is a "full-service" bioinformatics
center for the design of microarray studies and the analysis
of microarray-generated data. This facility core develops and
maintains a gene expression database and manages a bioinformatics
and statistical software suite. Members also provide on-site
user support, conduct tutorials and workshops on microarray data
analysis, and provide comprehensive data management and analysis.
Services
Specific services include, but are not limited to:
- Consultation on experimental design
- General statistical consulting
- Data management and preparation
- Custom software design and
development
- Biostatistics and bioinformatics support for all
types of microarray platforms: two-color cDNA, one-color and
two-color oligonucleotide,
Affymetrix
- Microarray data normalization and identification
of differentially expressed genes
- Microarray data visualization
and exploratory analysis (e.g., clustering)
- Data analysis,
interpretation, and report preparation
- Assistance on grant
or protocol submission (e.g., preparing statistical analysis
plan or database description)
- Manuscript review and preparation
- Advanced training on microarray
analysis
Experimental
Design
A successful microarray experiment depends on having a well-planned
and carefully designed study. Design decisions include the conditions
and tissues to select for study, the amount of biological and
technical replication, the sample size, and whether to use an
mRNA pooling strategy. Typically, different choices have advantages
and disadvantages, and these must be evaluated in light of the
primary goals of a particular scientific project. There is no
universally “best” microarray design. The Bioinformatics
and Biostatistics Facility Core evaluates candidate designs to
identify the most suitable design for a given study’s scientific
goals. A good microarray design will make the most of expensive
resources by maximizing precision while controlling costs.
Statistical
Analysis
Statistical analysis and data normalization are carried out
with several software packages:
- Spot-On
software developed at the University of Washington by Dr. Roger
Bumgarner[2]
- Spot,
a software package for the analysis of microarray images
from CSIRO, Australia's Commonwealth Scientific
and Industrial
Research Organisation
- MicroArray
Analysis of Variance (MA-ANOVA) software developed by the
Statistical Genetics Group at the
Jackson Laboratory[3]
- Bioconductor
software developed by a world wide group of collaborators. Core
funding and resources are based at the Biostatistics Unit
of the Dana Farber Cancer Institute
at Harvard
Medical School/Harvard School of Public Health[4]
- GeneSpring™,
produced by Silicon Genetics, Redwood City, California
- GeneTraffic ®,
produced by Iobion Informatics, La Jolla, CA.
These
software tools cover the range of tasks for microarrays, from
image analysis to normalization to statistical analysis.
Through these software packages the Core has access to
state-of-the-art methodology for microarray data analysis,
including methods
that have appeared in the literature in only the past
few years. Members
of the Facility Core are active members of the research
community working to develop better methods for microarray
data analysis. References
- Kerr
and Churchill. 2001. Experimental design for gene expression
microarrays. Biostatistics 2:183-201.
- Geiss
GK, Bumgarner RE, An MC, Agy MB, van’t Wout AB, Hammersmark
E, Carter VS, Upchurch D, Mullins JI, Katze MG. 2000. Large-scale
monitoring of host cell gene expression during HIV-1 infection
using cDNA microarrays. Virology 266:8-16.
- http://www.jax.org/staff/churchill/labsite/index.html
- http://www.bioconductor.org/
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Contact
Theo
Bammler,
PhD, Bioinformatics Coordinator
tbammler@u.washington.edu
(206) 616-7378
UW Box 354695
Dick Beyer, PhD,
Research Scientist
dbeyer@u.washington.edu
(206) 616-7378
UW Box 354695 |
