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

Asli N Goktug,Su Sien Ong,Taosheng Chen,Gajendra P S Raghava

doi:10.1371/journal.pone.0049386

Asli N Goktug, Su Sien Ong + Show 2 more

Open Access

https://doi.org/10.1371/journal.pone.0049386

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Journal: PLoS ONE	Publication Date: Nov 20, 2012
Citations: 39	License type: CC BY 4.0

Affiliation: St. Jude Children's Research Hospital

Abstract

BackgroundHigh-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.ResultsThe 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.ConclusionWith 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/.

Highlights

High-throughput RNA interference (RNAi) screening has become a widely used approach to elucidating gene functions
A new statistical parameter, strictly standardized mean difference (SSMD), proposed by Zhang [10,11] has become a widely used criterion for both screen quality control (QC) and hit selection, because the previously mentioned methods are associated with certain statistical drawbacks for the analysis of highthroughput screening data
SSMD addresses the magnitude of the RNAi effect and is more robust to sample size, which leads to comparable values across screens [12,13]

Summary

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 ttest 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 written in HTML format for easy access, and a comprehensive summary of screening results is written into tabdelimited output files

Conclusion

Background

Results and Discussion

Conclusions