A probability-based approach for the analysis of large-scale RNAi screens

By Renate König, Chih-yuan Chiang, Buu Tu, S. F. Yan, Paul DeJesus, Angelica Romero, T. Bergauer, A. Orth, U. Krueger, Yingyao Zhou and 1 more. Nature Methods, 2007

358 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5205fa82299cd566cf7c2966848a006ae3ad052d

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Citations in the corpus

Interferon Receptor Signaling Pathways Regulating PD-L1 and PD-L2 Expression (2017, positive): “For the shRNA screening, a probability-based RSA analysis was performed in order to minimize the impact of off-target activities of the different shRNA hairpins used in the study (König et al., 2007).”
Statistical Methods for Analysis of High-Throughput RNA Interference Screens (2009, methodology): “The redundant siRNA activity (RSA) analysis method 35 is appropriate for researchers seeking to integrate information about multiple RNAi reagents tested for each gene.”
Project DRIVE: A Compendium of Cancer Dependencies and Synthetic Lethal Relationships Uncovered by Large-Scale, Deep RNAi Screening. (2017, neutral): “RSA uses all shRNA reagents against a given gene to calculate a statistical significance that knockdown of gene X leads to loss of viability (König et al., 2007).”
Human Host Factors Required for Influenza Virus Replication (2010, neutral): “…(WSN-Ren), and luciferase readings were taken after 12, 24, and 36h. Data from two independent screens were analyzed using an integrative data analysis approach, which included Redundant siRNA Activity (RSA), as well as interactome and ontology-based analyses, (see Supplementary Information)6, 14.”
Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells (2014, background): “PLX day 7 (2) on the x-axis with PLX day 14 (1) on the y-axis.”
Meta- and Orthogonal Integration of Influenza “OMICs” Data Defines a Role for UBR4 in Virus Budding (2015, methodology): “We applied a statistical analysis to each screen set, termed the RSA algorithm, that utilizes an iterative accumulative hypergeometric distribution formula (König et al., 2007), to obtain a Z score for each gene in each individual screen (Figure 1, blue circles).”
Global analysis of host-pathogen interactions that regulate early stage HIV-1 replication (2008, methodology): “Since the primary screen was executed in an arrayed format, we were able to employ Redundant siRNA Analysis (RSA) to identify genes that were significantly inhibited by at least two independent siRNAs, many of which possessed reproducible, but moderate, activities (45% or greater reduction of HIV in”
Subtype-specific genomic alterations define new targets for soft tissue sarcoma therapy (2010, neutral): “25), we identified 99 genes whose knockdown significantly decreased cell growth in at least one cell line (nominal p<0.05; Supplementary Table 6).”
Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR (2015, methodology): “Several algorithms are developed for screening analysis on microarray or high-throughput sequencing data, such as RIGER [7], RSA [8], HitSelect [9], as well as the MAGeCK algorithm we previously developed [10].”