I. Microarray Related Links
1. Microarray Platforms
Affymetrix is a high-density
oligonucleotide GeneChip manufacturer. The Barley1 GeneChip is the first
Affymetrix high-density GeneChip for cereals. Affymetrix produces
GeneChips for a wide range of organisms, including barley, Arabidopsis, C.
elegans, yeast, human, rat, Drosophila, and E. coli.
used by Pat Brown's laboratory at Stanford University, when spotted arrays
consisted of cDNA representations of between 100 and 700 base pairs. Now, there
custom oligonucleotide sets representing cDNAs developed and
available for spotting from manufacturers such as
PGA Harvard and
2. Microarray Data Analysis Tools Used in BarleyBase
Bioconductor/R : Bioconductor
is an open source project aimed at providing comprehensive capability for
microarray data analysis, visualization and annotation. It started in fall
of 2001, and quickly evolved into a high-profile projects. It provides
packages for analyzing both Affymetrix oligo GeneChip data (affy, affydata
and affycomp packages) and cDNA spotted microarray.
BarleyBase extensively uses
R/Bioconductor in microarray data normalization, visualization and
online real-time analysis. BarleyBase used its Bioconductor's affy package for estimation of expression values by Robust Multi-chip
Average (RMA) and MAS5.0 methods. Dr. Dan Nettleton
explained how RMA normalization works.
Bioconductor is developed with
R, R is a
GNU project, an open
language and environment for statistical computing. It is a functional
programming language and has powerful graphical and visualization
MAS5.0: Affymetrix provides with
its Microarray Analysis Suite 5.0 the function to do absolute and
comparative expression estimation. MAS5.0 uses statistical algorithm for
normalization and calculate the expression values, the p-value and the
presence/absence call. BarleyBase uses the affy package of Bioconductor
for approximation of MAS5.0 methods in BarleyBase.
3. Microarray Databases
4. Microarray Database System
BioArray Software Environment (BASE) is a comprehensive
free web-based database solution for management and analysis
microarray analysis data.
at NCGR, GeneX-Lite is a client application that provides an interface to
a relational database management system (RDBMS). The client application
interface allows the user to load, manage, analyze, visualize and query
gene expression data.
5. Microarray Database Standard
Minimum information about a microarray experiment(
MIAME) is a
set of guidelines that can assist with the development of microarray
repositories and data analysis tools. It was Endorsed by
Microarray Gene Expression Data group
Now it is accepted by major scientific journals including Nature and
Science and adapted by many microarray databases.
Other Microarray Related Links:
The above-mentioned links are very limited in
range. So please trying some general link page to expand your reach:
II. Genome Databases and
1. Barley Related Links
2. Other Plant Related Links
III. Iowa State