HC StratoMineR: A Web-Based Tool for the Rapid Analysis of High-Content Datasets

Wienand A. Omta, Roy G. Van Heesbeen, Romina J. Pagliero, Lieke M. Van Der Velden, Daphne Lelieveld, Mehdi Nellen, Maik Kramer, Marley Yeong, Amir M. Saeidi, Rene H. Medema, Marco Spruit, Sjaak Brinkkemper, Judith Klumperman, David A. Egan

Research output: Contribution to journalArticlepeer-review

Abstract

High-content screening (HCS) can generate large multidimensional datasets and when aligned with the appropriate data mining tools, it can yield valuable insights into the mechanism of action of bioactive molecules. However, easy-to-use data mining tools are not widely available, with the result that these datasets are frequently underutilized. Here, we present HC StratoMineR, a web-based tool for high-content data analysis. It is a decision-supportive platform that guides even non-expert users through a high-content data analysis workflow. HC StratoMineR is built by using My Structured Query Language for storage and querying, PHP: Hypertext Preprocessor as the main programming language, and jQuery for additional user interface functionality. R is used for statistical calculations, logic and data visualizations. Furthermore, C++ and graphical processor unit power is diffusely embedded in R by using the rcpp and rpud libraries for operations that are computationally highly intensive. We show that we can use HC StratoMineR for the analysis of multivariate data from a high-content siRNA knock-down screen and a small-molecule screen. It can be used to rapidly filter out undesirable data; to select relevant data; and to perform quality control, data reduction, data exploration, morphological hit picking, and data clustering. Our results demonstrate that HC StratoMineR can be used to functionally categorize HCS hits and, thus, provide valuable information for hit prioritization.
Original languageEnglish
Pages (from-to)439-452
Number of pages14
JournalAssay and Drug Development Technologies
Volume14
Issue number8
DOIs
Publication statusPublished - 1 Oct 2016
Externally publishedYes

Keywords

  • Datamining
  • HCS
  • multiparametric
  • workflow

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