Title
TagSmart: analysis and visualization for yeast mutant fitness data measured by tag microarrays.
Abstract
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.
Year
DOI
Venue
2007
10.1186/1471-2105-8-128
BMC Bioinformatics
Keywords
Field
DocType
experimental design,algorithms,data analysis,open reading frame,microarrays,bioinformatics,robust statistics
Biology,Visualization,Open reading frame,Yeast,Protein Array Analysis,Saccharomyces cerevisiae,Bioinformatics,Mutant,Genetics,DNA microarray,Mutation
Journal
Volume
Issue
ISSN
8
1
1471-2105
Citations 
PageRank 
References 
14
0.35
1
Authors
6
Name
Order
Citations
PageRank
Chulyun Kim11057.77
Sangkyum Kim217810.54
Russell Dorer3140.35
Dan Xie4191.71
Jiawei Han579932.38
Sheng Zhong62019144.16