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Microarray Data Analysis

Microarrays are a new technology to investigate the expression levels of thousands of genes simultaneously. Microarrays present new statistical problems because the data is very high dimensional with very little replication. Methods of adjustment for multiple testing therefore become extremely important. Microarrays offer an exciting entry point for statisticians into the modern areas of computational biology and bioinformatics. This page focuses on cDNA microarrays although there is some information about Affymetrix microarrays at the bottom of the page.

• Annotation. Annotation resources.
• Conferences.
• Data.
• Database Systems. For storing, analysing and comparing microarray data.
• References. Technical reports and published papers on statistical analysis of microarray experiments.
• Research Groups. International groups specializing in statistical analysis of microarrays.
• Image Analysis Software. Software for scanning and image analysis of microarrays.
• Analysis Software.
• Journals.

Microarray Tutorials

• Anatomy of a Comparative Gene Expression Study. A tutorial on cDNA microarrays and comparative hybridization by Jeremy Buhler, University of Washington.
• DNA Microarray Technology - Flash Animation. Malcolm Campbell, Davidson College.
• Statistics in Genetics. Terry Speed's lecture notes at the University of California, Berkeley.
• CAMDA: Critical Assessment of Microarray Data Analysis. An annual competition. Bioinformatics Shared Resource, Duke University.
• Gershon, D. (2002). Microarray technology: An array of opportunities. Nature 416, 885 - 891; doi:10.1038/416885a.

Microarray Technology Resources

• BioChipNet. Information database on microarray technology. Natural and Medical Sciences Institute of the University of Tübingen, Transfer GmbH.
• BioMirror.
• Brown Lab. Pat Brown's home page at Stanford University. One of the pioneers of microarray research.
• Genome Chip. Basic information on DNA microarray technology and a list of academic and industrial links. Leming Shi.
• GenomeWeb. Large heirarchical directory of genome related links. Follow nucleic acids > gene expression to find the microarray links.
• GRID IT: Resources of Microarrays. A directory of resources on microarrays. Ruth Alscher, Virginia University of Technology.
• Institute for Genomic Research.
• Microarray Informatics at the European Bioinformatics Institute. Includes many data sets for download.
• EBI Microarray Discussion List. Archives of the list established by the European Bioinformatics Institute. Sangsoo Kim, Korean Research Institute of Bioscience and Biotechnology.
• Microarray.org. Information and tools.
• National Center for Genome Resources.
• National Institutes of Health.
  • Center for Information Technology.
    • Analytic Biostatistics Section.
  • National Human Genome Research Institute. 
  • National Institute on Aging.
    • NIA/NIH Mouse Genomics.
      • Mouse cDNA Project.
      • Database Search Engine.
• Stratagene. Universal reference mouse and human RNA.
• Y F Leung's Functional Genomics Page. Extensive resources on a number of topics including microarrays. Leung Yuk Fai, Chinese University of Hong Kong.

Australian Microarray Production Laboratories

• Australian Genome Research Facility. Melbourne.
• Clive and Vera Ramaciotti Centre for Gene Function Analysis. Includes a directory of links to microarray resources world-wide. University of New South Wales, Sydney.
• Gene CRC. A cooperative research centre funded by the Australian government bringing together the Institute for Molecular Bioscience, the Murdoch Children's Research Institute, the Queensland Institute of Medical Research and the Walter and Eliza Hall Institute of Medical Research.
• Institute for Molecular Bioscience. Brisbane.
• Peter MacCallum Cancer Institute Microarray Facility. Phone list. Melbourne.
• University of Adelaide, Molecular Biosciences, Microarray Facility. Adelaide.
• WA State Microarray Facility. Perth.

Clone Libraries

• Compugen OligoLibraries.

Microarray Technologies

• Spotted cDNA. Suitable for home-made arrays.
• Spotted long oligo. Suitable for home-made arrays.
• Agilent
• Applied Biosystems.
• Millennium Science. Affymetrix suppliers for Australia.

Affymetrix Genechip® data

• Affymetrix.
  • Whitepapers. Includes description of statistical algorithms
• Genelogic Workshop on Low Level Analysis of Affymetrix Genechip® data. Held in Bethesda, Maryland on November 19, 2001. Brief summary of papers and discussions.
• Expression Analysis. Commercial company offering processing and analysis of Affymetrix GeneChips.
• dCHIP.
• Genelogic data.
• Fred Wright's data.
• BrainArray custom CDF files for Affymetrix GeneChips.