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I. Microarray Related Links

1. Microarray Platforms

  • Affymetrix GeneChips: 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.
  • Spotted Microarrays:  Originally 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 are also custom oligonucleotide  sets representing cDNAs developed and available for spotting from manufacturers such as Incyte, Operon, PGA Harvard and MWG.

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 capabilities.

  • 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

  • ArrayExpress: The ArrayExpress Database located at European Bioinformatics Institute (EBI). It featured a MIAME-compliant submission tool, MIAME-Express.
  • GEDP: The Gene Expression Data Portal at NCI. Designed for human and rat microarray data, features a pathway-based query tool.
  • GEO: Gene Expression Omnibus (GEO) is provided by National Center for Biotechnology Information (NCBI), it is a public for data deposition and queries.
  • GXD: Dedicated to mouse and maintained by The Jackson Laboratory.
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  • NASCArray: The Nottingham Arabidopsis Stock Centre's (NASC) microarray database which is highly compatible with ArrayExpress. BarleyBase host some of the Arabidopsis ATH1 GeneChip data from NASC.

  • RAD: RAD (RNA Abundance Database) at University of Pennsylvania.

  • RMOS: Rice Microarray Opening Site (RMOS) for Rice Microarray Project. The microarray is spotted cDNA array.
  • SMD: Stanford Microarray Database, is the one of the earliest microarray database. The data are mainly spotted cDNA microarray data.
  • TAIR: It has a Microarray Elements Search and Download page which access Arabidopsis microarray data coming mostly from SMD.

4. Microarray Database System

  • BASE: BioArray Software Environment (BASE) is a comprehensive free web-based database solution for management and analysis microarray analysis data.
  • GeneX-Lite-: Developed 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

  • MIAME: 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 (MGED. Now it is accepted by major scientific journals including Nature and Science and adapted by many microarray databases.

6. Other Microarray Related Links:

The above-mentioned links are very limited in range. So please trying some general link page to expand your reach:

  • SMD Microarray Links : Software & tools, databases.
  • Gene Expression Links
  • Listing of DNA microarray links
  • Plant Arrays (Stanford)
  • National Cancer Institute

II. Genome Databases and Related Links

1. Barley Related Links

  • Barley Genome Dynamics (Schulman Group)
  • Barley genomics (Kleinhofs group)
  • cerealsDB.uk.net (Keith Edwards)
  • North American Barley Genome Project

2. Other Plant Related Links
  • Arizona Genomics Institute
  • Cereal Genomics and Pathology (Wise group)
  • Clemson University Genomics Institute
  • Databases for Molecular Biology
  • GrainGenes
  • Gramene
  • HarvEST
  • IPK Gatersleben
  • IACR - Long Ashton
  • Max Planck Institute, Koln
  • NASC - Nottingham Arabidopsis Stock Centre
  • National Plant Germplasm System
  • NCBI [National Center for Biotechnology Information]
  • PlantGDB
  • Risø National Laboratory
  • Scottish Crop Research Institute
  • Sputnik
  • TAIR
  • TIGR, The Institute for Genomic Research
  • TREP - Triticeae Repeat Sequence Database
  • UK Cropnet

III. Iowa State University Links

  • Bioinformatics and Computational Biology
  • Center for Plant Genomics
  • Center for Plant Responses to Stress
  • Center for Plant Transformation and Gene expression
  • Iowa State University Homepage
  • Laurence H. Baker Center for Bioinformatics and Biological Statistics
  • Plant Pathology
  • Plant Sciences Institute

 
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