TagSmart: analysis and visualization for yeast mutant fitness data measured by tag microarrays

<p>Abstract</p> <p>Background</p> <p>A nearly complete collection of gene-deletion mutants (96% of annotated open reading frames) of the yeast <it>Saccharomyces cerevisiae </it>has been systematically constructed. Tag microarrays are widely used to measure t...

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Main Authors: Xie Dan, Dorer Russell, Kim Sangkyum, Kim Chulyun, Han Jiawei, Zhong Sheng
Format: Article
Language:English
Published: BMC 2007-04-01
Series:BMC Bioinformatics
Online Access:http://www.biomedcentral.com/1471-2105/8/128
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spelling doaj-664d3b8dba2c444fb5e674c9d18e096e2020-11-24T21:06:02ZengBMCBMC Bioinformatics1471-21052007-04-018112810.1186/1471-2105-8-128TagSmart: analysis and visualization for yeast mutant fitness data measured by tag microarraysXie DanDorer RussellKim SangkyumKim ChulyunHan JiaweiZhong Sheng<p>Abstract</p> <p>Background</p> <p>A nearly complete collection of gene-deletion mutants (96% of annotated open reading frames) of the yeast <it>Saccharomyces cerevisiae </it>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.</p> <p>Results</p> <p>TagSmart is a web application for analysis and visualization of <it>Saccharomyces cerevisiae </it>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.</p> <p>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.</p> <p>Conclusion</p> <p>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: <url>http://biocomp.bioen.uiuc.edu/tagsmart</url></p> http://www.biomedcentral.com/1471-2105/8/128
collection DOAJ
language English
format Article
sources DOAJ
author Xie Dan
Dorer Russell
Kim Sangkyum
Kim Chulyun
Han Jiawei
Zhong Sheng
spellingShingle Xie Dan
Dorer Russell
Kim Sangkyum
Kim Chulyun
Han Jiawei
Zhong Sheng
TagSmart: analysis and visualization for yeast mutant fitness data measured by tag microarrays
BMC Bioinformatics
author_facet Xie Dan
Dorer Russell
Kim Sangkyum
Kim Chulyun
Han Jiawei
Zhong Sheng
author_sort Xie Dan
title TagSmart: analysis and visualization for yeast mutant fitness data measured by tag microarrays
title_short TagSmart: analysis and visualization for yeast mutant fitness data measured by tag microarrays
title_full TagSmart: analysis and visualization for yeast mutant fitness data measured by tag microarrays
title_fullStr TagSmart: analysis and visualization for yeast mutant fitness data measured by tag microarrays
title_full_unstemmed TagSmart: analysis and visualization for yeast mutant fitness data measured by tag microarrays
title_sort tagsmart: analysis and visualization for yeast mutant fitness data measured by tag microarrays
publisher BMC
series BMC Bioinformatics
issn 1471-2105
publishDate 2007-04-01
description <p>Abstract</p> <p>Background</p> <p>A nearly complete collection of gene-deletion mutants (96% of annotated open reading frames) of the yeast <it>Saccharomyces cerevisiae </it>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.</p> <p>Results</p> <p>TagSmart is a web application for analysis and visualization of <it>Saccharomyces cerevisiae </it>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.</p> <p>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.</p> <p>Conclusion</p> <p>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: <url>http://biocomp.bioen.uiuc.edu/tagsmart</url></p>
url http://www.biomedcentral.com/1471-2105/8/128
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