Integrating Experimental and Analytic Approaches to Improve Data Quality in Genome-wide RNAi Screens

Zhang, Xiaohua Douglas; Espeseth, Amy S.; Johnson, Eric N.; Chin, Jayne; Gates, Adam; Mitnaul, Lyndon J.; Marine, Shane; Tian, Jenny; Stec, Eric M.; Kunapuli, Priya; Holder, Dan; Heyse, Joseph F.; Strulovici, Berta; Ferrer, Marc

doi:10.1177/1087057108317145

Cited by 34 publications

(25 citation statements)

References 39 publications

(70 reference statements)

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“…To avoid generating another ad-hoc method, these methods have not been applied in any complete data sets. In a follow-up study, 32 Zhang and colleagues explore the implementation of the proposed SSMD-based QC methods, effective plate design, and the selection of effective controls in multiple real RNAi HTS experiments. The SSMDbased QC criteria and effective plate designs should be generally applicable to any assay where the endpoint is a difference in signal compared to a reference sample, including enzyme, receptor, and cellular function assays in addition to RNAi-based highthroughput screens.…”

Section: Discussionmentioning

confidence: 99%

Novel Analytic Criteria and Effective Plate Designs for Quality Control in Genome-Scale RNAi Screens

Zhang

2008

SLAS Discovery

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Section: Discussionmentioning

confidence: 99%

Novel Analytic Criteria and Effective Plate Designs for Quality Control in Genome-Scale RNAi Screens

Zhang

2008

SLAS Discovery

Self Cite

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“…The Z' factor has been proposed for reference in high-throughput screening to represent the response of an inhibitor or activator in a particular assay. If the value of the Z' factor exceeds 0.5, it indicates that the assay is viable [17][18][19][20][21] . We used ATP as the positive control and DMSO as the negative control to evaluate our HTS system.…”

Section: Validation Of the Hts Assaymentioning

confidence: 99%

Discovery of a novel inhibitor of NAD(P)+-dependent malic enzyme (ME2) by high-throughput screening

Wen

Fang-lei

et al. 2014

Acta Pharmacol Sin

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Aim: Malic enzymes are oxidative decarboxylases with NAD + or NAD(P) + as cofactor that catalyze the conversion of L-malate to pyruvate and CO 2 . The aim of this study was to discover and characterize a potent inhibitor of human NAD(P) + -dependent malic enzyme 2 (ME2). Methods: Recombinant human ME2-His-Tag fusion protein was overexpressed in E coli and purified with Ni-NTA resin. A highthroughput screening (HTS) assay was developed to find ME2 inhibitors. Detergent Brij-35 was used to exclude false positives. The characteristics of the inhibitor were analyzed with enzyme kinetics analysis. A thermal shift assay for ME2 was carried out to verify the binding of the inhibitor with the enzyme. Results: An HTS system for discovering ME2 inhibitors was established with a Z′ factor value of 0.775 and a signal-to-noise ratio (S/N) of 9.80. A library containing 12 683 natural products was screened. From 47 hits, NPD387 was identified as an inhibitor of ME2. The primary structure-activity relationship study on NPD387 derivatives showed that one derivative NPD389 was more potent than the parent compound NPD387 (the IC 50 of NPD389 was 4.63±0.36 μmol/L or 5.59±0.38 μmol/L, respectively, in the absence or presence of 0.01% Brij-35 in the assay system). The enzyme kinetics analysis showed that NPD389 was a fast-binding uncompetitive inhibitor with respect to the substrate NAD + and a mixed-type inhibitor with respect to the substrate L-malate. Conclusion: NPD389 is a potent ME2 inhibitor that binds to the enzyme in a fast-binding mode, acting as an uncompetitive inhibitor with respect to the substrate NAD + and a mixed-type inhibitor with respect to the substrate L-malate.

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“…Our colleagues and we have applied the method of contrast variable for hit selection and quality control in high-throughput biotechnologies (Zhang 2007a(Zhang ,b, 2008a(Zhang ,b, 2009(Zhang , 2010a(Zhang ,b, 2011aZhang et al 2007Zhang et al , 2008Zhang et al , 2010Zhang et al , 2011Zhou et al 2008;Klinghoffer et al 2009;Zhang and Heyse 2009;Zhang, Marine, and Ferrer 2009;Zhao et al 2010). In this article, we will explore how to use the method of contrast variable in general biopharmaceutical research.…”

Section: Introductionmentioning

confidence: 96%

Contrast Variable for Group Comparisons in Biopharmaceutical Research

Zhang

Heyse

2012

Statistics in Biopharmaceutical Research

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Group comparisons can be conducted at three levels: (1) group means, (2) both group means and variabilities, and (3) group distributions. A traditional contrast is defined as a linear combination of group means; thus, traditional contrast analysis may only effectively address group comparisons in the first level. The concept of a contrast variable has recently been proposed. A contrast variable is defined as a linear combination of random variables (each variable representing random values in a group) instead of group means. Based on a contrast variable, we can use the mean of a contrast to address questions on group comparisons at the first level as in traditional contrast analysis. Meanwhile, we can use the ratio of mean to standard deviation of a contrast variable, that is, standardized mean of a contrast variable (SMCV), to effectively address questions at the second level. We can further use the probability that a contrast variable obtains a positive value, that is, c + -probability, to effectively address questions at the third level. In this article, we explore the use of contrast variable, SMCV, and c + -probability for comparing multiple groups in biopharmaceutical studies. Contrast variable, c + -probability, and SMCV are applicable in a comparison context with or without independence and with or without homoscedasticity.

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Integrating Experimental and Analytic Approaches to Improve Data Quality in Genome-wide RNAi Screens

Cited by 34 publications

References 39 publications

Novel Analytic Criteria and Effective Plate Designs for Quality Control in Genome-Scale RNAi Screens

Novel Analytic Criteria and Effective Plate Designs for Quality Control in Genome-Scale RNAi Screens

Discovery of a novel inhibitor of NAD(P)+-dependent malic enzyme (ME2) by high-throughput screening

Contrast Variable for Group Comparisons in Biopharmaceutical Research

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