ArticleBMC bioinformatics2013
ScreenSifter: analysis and visualization of RNAi screening data.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
10 citing papers in PubMed.
- Article
- Image-Based Screening for Stress Granule Regulators.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Red-COLA1: a human fibroblast reporter cell line for type I collagen transcription.Scientific reports · 2020Article
- A Chemically Defined Feeder-free System for the Establishment and Maintenance of the Human Naive Pluripotent State.Stem cell reports · 2019Article
- A genome-scale RNAi screen for genetic interactors of the dynein co-factor nud-2 in Caenorhabditis elegans.Scientific data · 2018Article
- SUV420H2 is an epigenetic regulator of epithelial/mesenchymal states in pancreatic cancer.The Journal of cell biology · 2018Article
- Incorporating interaction networks into the determination of functionally related hit genes in genomic experiments with Markov random fields.Bioinformatics (Oxford, England) · 2017Article
- Human genome-wide RNAi screen reveals host factors required for enterovirus 71 replication.Nature communications · 2016Article
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Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRNAi screening is a powerful method to study the genetics of intracellular processes in metazoans. Technically, the approach has been largely inspired by techniques and tools developed for compound screening, including those for data analysis. However, by contrast with compounds, RNAi inducing agents can be linked to a large body of gene-centric, publically available data. However, the currently available software applications to analyze RNAi screen data usually lack the ability to visualize associated gene information in an interactive fashion.
resultsHere, we present ScreenSifter, an open-source desktop application developed to facilitate storing, statistical analysis and rapid and intuitive biological data mining of RNAi screening datasets. The interface facilitates meta-data acquisition and long-term safe-storage, while the graphical user interface helps the definition of a hit list and the visualization of biological modules among the hits, through Gene Ontology and protein-protein interaction analyses. The application also allows the visualization of screen-to-screen comparisons.
conclusionsOur software package, ScreenSifter, can accelerate and facilitate screen data analysis and enable discovery by providing unique biological data visualization capabilities.
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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.