ArticleGenome biology2015
gespeR: a statistical model for deconvoluting off-target-confounded RNA interference screens.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- CRISPR technology in ovarian cancer research: advances from gene editing to precision diagnosis and therapy.Translational cancer research · 2026Review
- Uncovering hidden cancer self-dependencies through analysis of shRNA-level dependency scores.Scientific reports · 2024Article
- A fast lasso-based method for inferring higher-order interactions.PLoS computational biology · 2022Article
- Systematic identification of novel cancer genes through analysis of deep shRNA perturbation screens.Nucleic acids research · 2021Article
- High content genome-wide siRNA screen to investigate the coordination of cell size and RNA production.Scientific data · 2021Article
- Article
- Advances in high-throughput methods for the identification of virus receptors.Medical microbiology and immunology · 2020Review
- Host factor prioritization for pan-viral genetic perturbation screens using random intercept models and network propagation.PLoS computational biology · 2020Article
- Learning signaling networks from combinatorial perturbations by exploiting siRNA off-target effects.Bioinformatics (Oxford, England) · 2019Article
- Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration.Nature communications · 2018Article
- Improved pathway reconstruction from RNA interference screens by exploiting off-target effects.Bioinformatics (Oxford, England) · 2018Article
- Measuring inferential importance of taxa using taxon influence indices.Ecology and evolution · 2018Article
- Evaluation and control of miRNA-like off-target repression for RNA interference.Cellular and molecular life sciences : CMLS · 2018Review
- While it is not deliberate, much of today's biomedical research contains logical and technical flaws, showing a need for corrective action.International journal of medical sciences · 2018Review
- Defining a Cancer Dependency Map.Cell · 2017Article
- Seed-effect modeling improves the consistency of genome-wide loss-of-function screens and identifies synthetic lethal vulnerabilities in cancer cells.Genome medicine · 2017Article
- RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets.Nucleic acids research · 2017Article
- Article
- PubChem BioAssay: 2017 update.Nucleic acids research · 2017Article
- Outlier analysis of functional genomic profiles enriches for oncology targets and enables precision medicine.BMC genomics · 2016Article
Corrections and comments
- Erratum issued
Authors and funding
16 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small interfering RNAs (siRNAs) exhibit strong off-target effects, which confound the gene-level interpretation of RNA interference screens and thus limit their utility for functional genomics studies. Here, we present gespeR, a statistical model for reconstructing individual, gene-specific phenotypes. Using 115,878 siRNAs, single and pooled, from three companies in three pathogen infection screens, we demonstrate that deconvolution of image-based phenotypes substantially improves the reproducibility between independent siRNA sets targeting the same genes. Genes selected and prioritized by gespeR are validated and shown to constitute biologically relevant components of pathogen entry mechanisms and TGF-β signaling. gespeR is available as a Bioconductor R-package.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.