Tools for Microarray Data Analysis

• Expression Profiler at the European Bioinformatics Institute (EBI). "Expression Profiler is a set of tools for clustering, analysis and visualization of gene expression and other genomic data. Tools in the Expression Profiler allow to perform cluster analysis, pattern discovery, pattern visualization, study and search Gene Ontology categories, generate sequence logos, extract regulatory sequences, study protein interactions, as well as to link analysis results to external tools and databases."

• Cluster and TreeView programs created by Michael Eisen "Cluster and TreeView are an integrated pair of programs for analyzing and visualizing the results of complex microarray experiments."

• GeneCluster program created at the Whitehead Institute for Biomedical Research. "GeneCluster 1.0 is a standalone Java application implementing the methodology described in Tamayo et al. (1999). It provides the ability to 1) filter and preprocess data in a variety of ways, 2) cluster expression profiles using the SOM algorithm, and 3) view the results."

• J-Express program created at the Department of Informatics, University of Bergen, Norway. "J-Express is a java application for the analysis of gene expression data provided by microarray experiments. It is programmed for the java runtime environment 1.2, which is available for most operating systems. Methods included in the application are:
  • Hierarchical clustering
  • Self-organizing maps
  • Principal component analysis
  • K-means
  • Profile search
  • Integrated tools for visualisation."

Motif Discovery Tools

• AlignACE software created at the Church Lab, Harvard Medical School, Harvard University. "AlignACE (Aligns Nucleic Acid Conserved Elements) is a program which finds sequence elements conserved in a set of DNA sequences."

• The MEME/MAST system at the Computer Science and Engineering department, University of California, San Diego. "The MEME system allows you to
  1. discover motifs (highly conserved regions) in groups of related DNA or protein sequences using MEME and,
  2. search sequence databases using motifs using MAST."

• Regulatory Sequence Analysis Tools. "This site provides a series of modular computer programs specifically designed for the detection of regulatory signals in non-coding sequences. An increasing number of organisms are supported on this web site. We installed a few eukaryotes (Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana) and all the completely sequenced bacterial genomes (from Genbank)."

Arabidopsis databases

• The Arabidopsis Information Resource (TAIR). "The Arabidopsis Information Resource (TAIR) provides a comprehensive resource for the scientific community working with Arabidopsis thaliana, a widely used model plant. TAIR consists of a searchable relational database, which includes many different datatypes. The data can be viewed using our interactive MapViewer, and analyzed with our tools. Our datasets can also be downloaded for your convenience. In addition, pages on news, information on the Arabidopsis Genome Initiative (AGI), Arabidopsis lab protocols, and useful links are provided. TAIR is a collaboration between the Carnegie Institution of Washington Department of Plant Biology, Stanford, California, and the National Center for Genome Resources (NCGR), Santa Fe, New Mexico."

• MIPS Arabidopsis Thaliana DataBase (MATDB). "MIPS Arabidopsis thaliana database is the www access to data of the Arabidopsis Genome Initiative compiled, analysed, annotated and stored at MIPS by the MIPS Arabidopsis group. TIGR maintains an alternative Arabidopsis genome database."

• The TIGR Arabidopsis thaliana Database. This is a collection of information on Arabidopsis genome research at the Institute for Genomic Research (TIGR).