ArticleGenome research2013
ATARiS: computational quantification of gene suppression phenotypes from multisample RNAi screens.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers, 1 of them a synthesis that pooled it.
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Who cites it
83 citing papers in PubMed, 1 synthesis or guideline pooled it, 127 citations in OpenAlex.
- Pooled it
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- Discovery of synthetic lethal interactions from large-scale pan-cancer perturbation screens.Nature communications · 2022Article
- ZetaSuite: computational analysis of two-dimensional high-throughput data from multi-target screens and single-cell transcriptomics.Genome biology · 2022Article
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- Systematic identification of novel cancer genes through analysis of deep shRNA perturbation screens.Nucleic acids research · 2021Article
- Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge.PLoS computational biology · 2021Article
- A Covalent Calmodulin Inhibitor as a Tool to Study Cellular Mechanisms of K-Ras-Driven Stemness.Frontiers in cell and developmental biology · 2021Article
- Cancer biology functional genomics: From small RNAs to big dreams.Molecular carcinogenesis · 2020Article
- Proline rich 11 (PRR11) overexpression amplifies PI3K signaling and promotes antiestrogen resistance in breast cancer.Nature communications · 2020Article
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- Beta-binomial modeling of CRISPR pooled screen data identifies target genes with greater sensitivity and fewer false negatives.Genome research · 2019Article
- Efficient algorithms to discover alterations with complementary functional association in cancer.PLoS computational biology · 2019Article
- TranscriptAchilles: a genome-wide platform to predict isoform biomarkers of gene essentiality in cancer.GigaScience · 2019Article
- Genetic Screens Reveal FEN1 and APEX2 as BRCA2 Synthetic Lethal Targets.Molecular cell · 2019Article
23 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
14 authors at 1 institution in 1 country.
Funding
Abstract
Genome-scale RNAi libraries enable the systematic interrogation of gene function. However, the interpretation of RNAi screens is complicated by the observation that RNAi reagents designed to suppress the mRNA transcripts of the same gene often produce a spectrum of phenotypic outcomes due to differential on-target gene suppression or perturbation of off-target transcripts. Here we present a computational method, Analytic Technique for Assessment of RNAi by Similarity (ATARiS), that takes advantage of patterns in RNAi data across multiple samples in order to enrich for RNAi reagents whose phenotypic effects relate to suppression of their intended targets. By summarizing only such reagent effects for each gene, ATARiS produces quantitative, gene-level phenotype values, which provide an intuitive measure of the effect of gene suppression in each sample. This method is robust for data sets that contain as few as 10 samples and can be used to analyze screens of any number of targeted genes. We used this analytic approach to interrogate RNAi data derived from screening more than 100 human cancer cell lines and identified HNF1B as a transforming oncogene required for the survival of cancer cells that harbor HNF1B amplifications. ATARiS is publicly available at http://broadinstitute.org/ataris.
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What OpenQuestion holds
Registered trials
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.