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GUItars: A GUI Tool for Analysis of High-Throughput RNA Interference Screening Data

BACKGROUND: High-throughput RNA interference (RNAi) screening has become a widely used approach to elucidating gene functions. However, analysis and annotation of large data sets generated from these screens has been a challenge for researchers without a programming background. Over the years, numer...

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Detalles Bibliográficos
Autores principales: Goktug, Asli N., Ong, Su Sien, Chen, Taosheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3502531/
https://www.ncbi.nlm.nih.gov/pubmed/23185323
http://dx.doi.org/10.1371/journal.pone.0049386
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author Goktug, Asli N.
Ong, Su Sien
Chen, Taosheng
author_facet Goktug, Asli N.
Ong, Su Sien
Chen, Taosheng
author_sort Goktug, Asli N.
collection PubMed
description BACKGROUND: High-throughput RNA interference (RNAi) screening has become a widely used approach to elucidating gene functions. However, analysis and annotation of large data sets generated from these screens has been a challenge for researchers without a programming background. Over the years, numerous data analysis methods were produced for plate quality control and hit selection and implemented by a few open-access software packages. Recently, strictly standardized mean difference (SSMD) has become a widely used method for RNAi screening analysis mainly due to its better control of false negative and false positive rates and its ability to quantify RNAi effects with a statistical basis. We have developed GUItars to enable researchers without a programming background to use SSMD as both a plate quality and a hit selection metric to analyze large data sets. RESULTS: The software is accompanied by an intuitive graphical user interface for easy and rapid analysis workflow. SSMD analysis methods have been provided to the users along with traditionally-used z-score, normalized percent activity, and t-test methods for hit selection. GUItars is capable of analyzing large-scale data sets from screens with or without replicates. The software is designed to automatically generate and save numerous graphical outputs known to be among the most informative high-throughput data visualization tools capturing plate-wise and screen-wise performances. Graphical outputs are also written in HTML format for easy access, and a comprehensive summary of screening results is written into tab-delimited output files. CONCLUSION: With GUItars, we demonstrated robust SSMD-based analysis workflow on a 3840-gene small interfering RNA (siRNA) library and identified 200 siRNAs that increased and 150 siRNAs that decreased the assay activities with moderate to stronger effects. GUItars enables rapid analysis and illustration of data from large- or small-scale RNAi screens using SSMD and other traditional analysis methods. The software is freely available at http://sourceforge.net/projects/guitars/.
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spelling pubmed-35025312012-11-26 GUItars: A GUI Tool for Analysis of High-Throughput RNA Interference Screening Data Goktug, Asli N. Ong, Su Sien Chen, Taosheng PLoS One Research Article BACKGROUND: High-throughput RNA interference (RNAi) screening has become a widely used approach to elucidating gene functions. However, analysis and annotation of large data sets generated from these screens has been a challenge for researchers without a programming background. Over the years, numerous data analysis methods were produced for plate quality control and hit selection and implemented by a few open-access software packages. Recently, strictly standardized mean difference (SSMD) has become a widely used method for RNAi screening analysis mainly due to its better control of false negative and false positive rates and its ability to quantify RNAi effects with a statistical basis. We have developed GUItars to enable researchers without a programming background to use SSMD as both a plate quality and a hit selection metric to analyze large data sets. RESULTS: The software is accompanied by an intuitive graphical user interface for easy and rapid analysis workflow. SSMD analysis methods have been provided to the users along with traditionally-used z-score, normalized percent activity, and t-test methods for hit selection. GUItars is capable of analyzing large-scale data sets from screens with or without replicates. The software is designed to automatically generate and save numerous graphical outputs known to be among the most informative high-throughput data visualization tools capturing plate-wise and screen-wise performances. Graphical outputs are also written in HTML format for easy access, and a comprehensive summary of screening results is written into tab-delimited output files. CONCLUSION: With GUItars, we demonstrated robust SSMD-based analysis workflow on a 3840-gene small interfering RNA (siRNA) library and identified 200 siRNAs that increased and 150 siRNAs that decreased the assay activities with moderate to stronger effects. GUItars enables rapid analysis and illustration of data from large- or small-scale RNAi screens using SSMD and other traditional analysis methods. The software is freely available at http://sourceforge.net/projects/guitars/. Public Library of Science 2012-11-20 /pmc/articles/PMC3502531/ /pubmed/23185323 http://dx.doi.org/10.1371/journal.pone.0049386 Text en © 2012 Goktug et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Goktug, Asli N.
Ong, Su Sien
Chen, Taosheng
GUItars: A GUI Tool for Analysis of High-Throughput RNA Interference Screening Data
title GUItars: A GUI Tool for Analysis of High-Throughput RNA Interference Screening Data
title_full GUItars: A GUI Tool for Analysis of High-Throughput RNA Interference Screening Data
title_fullStr GUItars: A GUI Tool for Analysis of High-Throughput RNA Interference Screening Data
title_full_unstemmed GUItars: A GUI Tool for Analysis of High-Throughput RNA Interference Screening Data
title_short GUItars: A GUI Tool for Analysis of High-Throughput RNA Interference Screening Data
title_sort guitars: a gui tool for analysis of high-throughput rna interference screening data
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3502531/
https://www.ncbi.nlm.nih.gov/pubmed/23185323
http://dx.doi.org/10.1371/journal.pone.0049386
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