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Overview of Microarray Data Visualization Programs

This article provides an overview of various software packages available for microarray data visualization, including Cluster/Treeview, GeneSpring, GeneSight, Spotfire, Resolver, Lucidea, and many others. The general functions of these programs include data normalization, graphing/filtering capabilities, clustering (hierarchical, SOMs, K-Means), and principal component analysis. The article also discusses different genome formats supported by GeneSpring and provides examples of tissue-specific clustering.

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Overview of Microarray Data Visualization Programs

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  1. Overview of Microarray Data Visualization Programs Jeff Landgraf Arabidopsis Functional Genomics Consortium MSU-DOE Plant Research Laboratory Michigan State University

  2. Software packages for data visualization • Cluster/Treeview- Mike Eisen • GeneSpring- Silicon Genetics • GeneSight- Biodiscovery • Spotfire- Spotfire • Resolver- Rosetta Inpharmatics • Lucidea- Amersham/Pharmacia Biotech • Many others…

  3. General Functions • Data normalization • Various graphing/filtering capabilities • Clustering • Hierarchical • SOMs • K-Means • Principal component analysis

  4. Genome Formats- GeneSpring • “name list” • single column list of gene names • “name function” • gene name + function • “mapped” • systematic name, common name, map position, EC number, description, product, phenotype, function, keywords, GenBank locus, synonym, sequence, custom

  5. Tissue Specific Cluster F/C L/C R/C Si/C St/C

  6. MSU-Microarray Lab Ellen Wisman Robert Schaffer Monica Accerbi Verna Simon Scott Lewis Kim Trouten David Green Pieter Steenhuis Green Lab Pam Green Rodrigo Gutierrez Acknowledgements

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