TagSmart: analysis and visualization for yeast mutant fitness data measured by tag microarrays
1 Department Computer Science, University of Illinois at Urbana Champaign, Urbana, IL, USA
2 Department of Bioengineering, University of Illinois at Urbana Champaign, Urbana, IL, USA
3 Department of Pathology, Virginia Mason Medical Center, 1100 Ninth Avenue, Seattle, WA, USA
4 Department of Statistics, University of Illinois at Urbana Champaign, Champaign, IL, USA
5 Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, USA
6 School of Electrical Engineering and Computer Science, Seoul National University, South Korea
BMC Bioinformatics 2007, 8:128 doi:10.1186/1471-2105-8-128Published: 18 April 2007
A nearly complete collection of gene-deletion mutants (96% of annotated open reading frames) of the yeast Saccharomyces cerevisiae has been systematically constructed. Tag microarrays are widely used to measure the fitness of each mutant in a mutant mixture. The tag array experiments can have a complex experimental design, such as time course measurements and drug treatment with multiple dosages.
TagSmart is a web application for analysis and visualization of Saccharomyces cerevisiae mutant fitness data measured by tag microarrays. It implements a robust statistical approach to assess the concentration differences among S. cerevisiae mutant strains. It also provides an interactive environment for data analysis and visualization. TagSmart has the following advantages over previously described analysis procedures: 1) it is user-friendly software rather than merely a description of analytical procedure; 2) It can handle complicated experimental designs, such as multiple time points and treatment with multiple dosages; 3) it has higher sensitivity and specificity; 4) It allows users to mask out "bad" tags in the analysis.
Two biological tests were performed to illustrate the performance of TagSmart. First, we generated titration mixtures of mutant strains, in which the relative concentration of each strain was controlled. We used tag microarrays to measure the numbers of tag copies in each titration mixture. The data was analyzed with TagSmart and the result showed high precision and recall. Second, TagSmart was applied to a dataset in which heterozygous deletion strain mixture pools were treated with a new drug, Cincreasin. TagSmart identified 53 mutant strains as sensitive to Cincreasin treatment. We individually tested each identified mutant, and found 52 out of the 53 predicted mutants were indeed sensitive to Cincreasin.
TagSmart is provided "as is" to analyze tag array data produced by Affymetrix and Agilent arrays. TagSmart web application is assessable by Windows, Mac, and Linux users. It also has a downloadable version for execution on PCs running Windows. TagSmart is available for academic use at: http://biocomp.bioen.uiuc.edu/tagsmart webcite