Introduction

Cutoff Finder is an easy–to–use web application for the determination of cutoff points in molecular data. Often, molecular data such as gene expression or protein expression data are represented by continuous or at least ordinal variables. In order to translate these variables into a clinical decision, it is necessary to determine a cutoff point and to stratify patients into two groups, each of which requiring a different kind of treatment. Cutoff Finder offers a multitude of methods for cutoff determination and plots.

License and citing

Cutoff Finder may be used freely and without any warranty of the developers. Cutoff calculations and plots can be used in scientific publications, but you are kindly asked to cite Budczies et al. (2012), PLoS ONE 7(12): e51862.

Documentation

A documentation of all cutoff optimization and plot methods can be found in the Cutoff Finder manual. A use case was presented as poster at the German Bioinformatics on Conference (GCB) 2011. A more comprehensive discussion of the software can be found in a recent publication.

Workflow

The data are processed as follows:

Cutoff Finder: Workflow
  1. The data are uploaded from a tab–separated File, rows representing patients and columns representing variables. Alternatively, one of three example data sets can be imported.
  2. The user selects the biomarker and optionally outcome and survival variables from the table columns.
  3. The user selects the method for cutoff determination.
  4. The user chooses the kinds of plots that should be generated.
  5. The inquiry is send to the statistical engine R. The optimal cutoff point is determined and analysis plots are generated.
  6. The user is directed to the results webpage, where cutoff point and plots are shown.