an interactive tool for analyzing drug combination dose-response data
SynergyFinder accepts two data formats: Table and Matrix.
In the Table format, the input dose-response matrix is represented as a table where each row contains the information about the one cell in the dose-response matrix (Fig.1).
The input table must contain the following columns:
The orders of rows and columns are arbitrary. The number of drug combinations (PairIndex) provided in the input file is unlimited. The only restriction is imposed on the size of a dose-response matrix, which should comprise at least three rows and columns, so that sensible synergy scores can be calculated.
Fig.1 Input file in Table format.
In the Matrix format, the dose-response matrix is represented in a matrix form with drug concentrations shown along the top and left side of the matrix (Fig.2).
The three rows should precede each dose-response matrix:
The drug concentrations should be located at the top and left side of the matrix, where left side concentrations correspond to Drug1 and concentrations shown at the top correspond to the Drug2. The number of drug combinations provided in the input file is unlimited. The only restriction is imposed on the dose-response matrix size, which should comprise at least three rows and columns, so that sensible synergy scores can be calculated.
Fig.2 An input file in Matrix format. Two dose-response matrices are provided as an example.
Using the “Browse” button, users could select a file from local directory for uploading. The expected file formats are:
Example data is available from here.
After uploading the input file the user needs to specify the type of phenotypic response. Available options in SynergyFinder are:
After specifying the type of phenotypic response the user may firstly obtain an overview of the provided data in a searchable table to check for the problematic data points.
By switching the “Visualize dose response data” toggle button, users will be directed to nex tab “Dose Response Map” for dose-response dat visualization.
This tab will show an overview of the full dose-response matrix, as well as the dose response (%inhibition) curve for the single drugs (i.e. the first column and first row in the dose-response matrix), fitted by four-parameter logistic curves. The tabs named by combination of drug names are design for navigating to maps for different combinations. (Fig.3)