The Use of Strictly Standardized Mean Difference for Hit Selection in Primary RNA Interference High-Throughput Screening Experiments

@article{Zhang2007TheUO,
  title={The Use of Strictly Standardized Mean Difference for Hit Selection in Primary RNA Interference High-Throughput Screening Experiments},
  author={Xiaohua Douglas Zhang and Marc Ferrer and Amy S. Espeseth and Shane D. Marine and Erica M. Stec and Michael A. Crackower and Daniel J. Holder and Joseph F. Heyse and Berta Strulovici},
  journal={Journal of Biomolecular Screening},
  year={2007},
  volume={12},
  pages={497 - 509}
}
RNA interference (RNAi) high-throughput screening (HTS) has been hailed as the 2nd genomics wave following the 1st genomics wave of gene expression microarrays and single-nucleotide polymorphism discovery platforms. Following an RNAi HTS, the authors are interested in identifying short interfering RNA (siRNA) hits with large inhibition/activation effects. For hit selection, the z-score method and its variants are commonly used in primary RNAi HTS experiments. Recently, strictly standardized… 

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References

SHOWING 1-10 OF 20 REFERENCES

A New Method with Flexible and Balanced Control of False Negatives and False Positives for Hit Selection in RNA Interference High-Throughput Screening Assays

The z-score method and its variants for testing mean difference are commonly used for hit selection in high-throughput screening (HTS) assays. Strictly standardized mean difference (SSMD) offers a

Improved Statistical Methods for Hit Selection in High-Throughput Screening

The authors describe and show numerous real examples from the biologist-friendly Stat Server® HTS application (SHS), a custom-developed software tool built on the commercially available S-PLUS and StatServer statistical analysis and server software that remotely processes HTS data using powerful and sophisticated statistical methodology.

A Simple Statistical Parameter for Use in Evaluation and Validation of High Throughput Screening Assays

A screening window coefficient, called "Z- factor," is defined, which is reflective of both the assay signal dynamic range and the data variation associated with the signal measurements, and therefore is suitable for assay quality assessment.

Statistical Analysis of Systematic Errors in High-Throughput Screening

A method for evaluating a background surface of an HTS assay is developed and it can be used to correct raw HTS data and take into account systematic errors that may affect the procedure of hit selection.

Statistical practice in high-throughput screening data analysis

It is argued that replicate measurements are needed to verify assumptions of current methods and to suggest data analysis strategies when assumptions are not met, and the integration of replicates with robust statistical methods in primary screens will facilitate the discovery of reliable hits, ultimately improving the sensitivity and specificity of the screening process.

Statistical and Graphical Methods for Quality Control Determination of High-Throughput Screening Data

The authors describe new QC methods and show numerous real examples from their biologist-friendly Stat Server® HTS application, a custom-developed software tool built from the commercially available S-PLUS and Stat Server statistical analysis and server software.

A cell-based beta-lactamase reporter gene assay for the identification of inhibitors of hepatitis C virus replication.

This report describes the development, optimization, and implementation of a cell-based assay for high-throughput screening (HTS) to identify inhibitors to hepatitis C virus (HCV) replication. The

Sensitized RNAi screen of human kinases and phosphatases identifies new regulators of apoptosis and chemoresistance

Evasion from apoptosis is a hallmark of cancer, and recent success using targeted therapeutics underscores the importance of identifying anti-apoptotic survival pathways. Here we utilize RNA