PhenoTimer: software for the visual mapping of time-resolved phenotypic landscapes

PLoS One. 2013 Aug 12;8(8):e72361. doi: 10.1371/journal.pone.0072361. eCollection 2013.


Timing common and specific modulators of disease progression is crucial for treatment, but the understanding of the underlying complex system of interactions is limited. While attempts at elucidating this experimentally have produced enormous amounts of phenotypic data, tools that are able to visualize and analyze them are scarce and the insight obtained from the data is often unsatisfactory. Linking and visualizing processes from genes to phenotypes and back, in a temporal context, remains a challenge in systems biology. We introduce PhenoTimer, a 2D/3D visualization tool for the mapping of time-resolved phenotypic links in a genetic context. It uses a novel visualization approach for relations between morphological defects, pathways or diseases, to enable fast pattern discovery and hypothesis generation. We illustrate its capabilities of tracing dynamic motifs on cell cycle datasets that explore the phenotypic order of events upon perturbations of the system, transcriptional activity programs and their connection to disease. By using this tool we are able to fine-grain regulatory programs for individual time points of the cell cycle and better understand which patterns arise when these programs fail. We also illustrate a way to identify common mechanisms of misregulation in diseases and drug abuse.

MeSH terms

  • Cell Cycle / physiology
  • Gene Expression Regulation
  • Genetic Association Studies / methods*
  • Genotype
  • Humans
  • Internet
  • Neoplasms / genetics
  • Neoplasms / metabolism
  • Phenotype
  • Software*
  • Substance-Related Disorders / genetics
  • Substance-Related Disorders / metabolism
  • Time Factors
  • User-Computer Interface

Grants and funding

This work was supported by TAMAHUD (LSHC-CT-2007-037472) and FORSYS-ViroQuant. MS was supported by the EMBL PhD Program. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.