Dataset Information

CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets.

ABSTRACT: Drug synergies are sought to identify combinations of drugs particularly beneficial. User-friendly software solutions that can assist analysis of large-scale datasets are required.CImbinator is a web-service that can aid in batch-wise and in-depth analyzes of data from small-scale and large-scale drug combination screens. CImbinator offers to quantify drug combination effects, using both the commonly employed median effect equation, as well as advanced experimental mathematical models describing dose response relationships.CImbinator is written in Ruby and R. It uses the R package drc for advanced drug response modeling. CImbinator is available at http://cimbinator.bioinfo.cnio.es , the source-code is open and available at https://github.com/Rbbt-Workflows/combination_index . A Docker image is also available at https://hub.docker.com/r/mikisvaz/rbbt-ci_mbinator/ .asmund.flobak@ntnu.no or miguel.vazquez@cnio.es.Supplementary data are available at Bioinformatics online.

SUBMITTER: Flobak A

PROVIDER: S-EPMC5860113 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets.

Flobak Åsmund Å Vazquez Miguel M Lægreid Astrid A Valencia Alfonso A

Bioinformatics (Oxford, England) 20170801 15

<h4>Motivation</h4>Drug synergies are sought to identify combinations of drugs particularly beneficial. User-friendly software solutions that can assist analysis of large-scale datasets are required.<h4>Results</h4>CImbinator is a web-service that can aid in batch-wise and in-depth analyzes of data from small-scale and large-scale drug combination screens. CImbinator offers to quantify drug combination effects, using both the commonly employed median effect equation, as well as advanced experime ...[more]

PMID: 28444126

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Project description:BackgroundDrug combinations have the potential to improve efficacy while limiting toxicity. To robustly identify synergistic combinations, high-throughput screens using full dose-response surface are desirable but require an impractical number of data points. Screening of a sparse number of doses per drug allows to screen large numbers of drug pairs, but complicates statistical assessment of synergy. Furthermore, since the number of pairwise combinations grows with the square of the number of drugs, exploration of large screens necessitates advanced visualization tools.ResultsWe describe a statistical and visualization framework for the analysis of large-scale drug combination screens. We developed an approach suitable for datasets with large number of drugs pairs even if small number of data points are available per drug pair. We demonstrate our approach using a systematic screen of all possible pairs among 108 cancer drugs applied to melanoma cell lines. In this dataset only two dose-response data points per drug pair and two data points per single drug test were available. We used a Bliss-based linear model, effectively borrowing data from the drug pairs to obtain robust estimations of the singlet viabilities, consequently yielding better estimates of drug synergy. Our method improves data consistency across dosing thus likely reducing the number of false positives. The approach allows to compute p values accounting for standard errors of the modeled singlets and combination viabilities. We further develop a synergy specificity score that distinguishes specific synergies from those arising with promiscuous drugs. Finally, we developed a summarized interactive visualization in a web application, providing efficient access to any of the 439,000 data points in the combination matrix ( http://www.cmtlab.org:3000/combo_app.html ). The code of the analysis and the web application is available at https://github.com/arnaudmgh/synergy-screen .ConclusionsWe show that statistical modeling of single drug response from drug combination data can help determine significance of synergy and antagonism in drug combination screens with few data point per drug pair. We provide a web application for the rapid exploration of large combinatorial drug screen. All codes are available to the community, as a resource for further analysis of published data and for analysis of other drug screens.

Dataset Information

CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets.

Publications

CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets.

Similar Datasets

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