title: HC StratoMineR: A Web-Based Tool for the Rapid Analysis of High-Content Datasets.
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.
authors.affiliation: 1 Department of Cell Biology, Centre for Molecular Medicine , UMC Utrecht, Utrecht, Netherlands .|2 Department of Information and Computing Sciences, Utrecht University , Utrecht, Netherlands .
authors.forename: Wienand A
authors.initials: WA
authors.lastname: Omta
authors.affiliation: 3 Department of Cell Biology, NKI-AVL , Amsterdam, Netherlands .
authors.forename: Roy G
authors.initials: RG
authors.lastname: van Heesbeen
authors.affiliation: 1 Department of Cell Biology, Centre for Molecular Medicine , UMC Utrecht, Utrecht, Netherlands .
authors.forename: Romina J
authors.initials: RJ
authors.lastname: Pagliero
authors.affiliation: 1 Department of Cell Biology, Centre for Molecular Medicine , UMC Utrecht, Utrecht, Netherlands .
authors.forename: Lieke M
authors.initials: LM
authors.lastname: van der Velden
authors.affiliation: 1 Department of Cell Biology, Centre for Molecular Medicine , UMC Utrecht, Utrecht, Netherlands .
authors.forename: Daphne
authors.initials: D
authors.lastname: Lelieveld
authors.affiliation: 1 Department of Cell Biology, Centre for Molecular Medicine , UMC Utrecht, Utrecht, Netherlands .
authors.forename: Mehdi
authors.initials: M
authors.lastname: Nellen
authors.affiliation: 1 Department of Cell Biology, Centre for Molecular Medicine , UMC Utrecht, Utrecht, Netherlands .
authors.forename: Maik
authors.initials: M
authors.lastname: Kramer
authors.affiliation: 1 Department of Cell Biology, Centre for Molecular Medicine , UMC Utrecht, Utrecht, Netherlands .
authors.forename: Marley
authors.initials: M
authors.lastname: Yeong
authors.affiliation: 2 Department of Information and Computing Sciences, Utrecht University , Utrecht, Netherlands .
authors.forename: Amir M
authors.initials: AM
authors.lastname: Saeidi
authors.affiliation: 3 Department of Cell Biology, NKI-AVL , Amsterdam, Netherlands .
authors.forename: Rene H
authors.initials: RH
authors.lastname: Medema
authors.affiliation: 2 Department of Information and Computing Sciences, Utrecht University , Utrecht, Netherlands .
authors.forename: Marco
authors.initials: M
authors.lastname: Spruit
authors.affiliation: 2 Department of Information and Computing Sciences, Utrecht University , Utrecht, Netherlands .
authors.forename: Sjaak
authors.initials: S
authors.lastname: Brinkkemper
authors.affiliation: 1 Department of Cell Biology, Centre for Molecular Medicine , UMC Utrecht, Utrecht, Netherlands .
authors.forename: Judith
authors.initials: J
authors.lastname: Klumperman
authors.affiliation: 1 Department of Cell Biology, Centre for Molecular Medicine , UMC Utrecht, Utrecht, Netherlands .
authors.forename: David A
authors.initials: DA
authors.lastname: Egan
mesh_terms: D016000:Cluster Analysis; D057225:Data Mining / Q000379:methods*; D016208:Databases, Factual / Q000706:statistics & numerical data*; D006367:HeLa Cells; D006801:Humans; D020407:Internet; D061986:MCF-7 Cells; D013223:Statistics as Topic / Q000379:methods*
keywords: HCS; datamining; multiparametric; workflow