High-Throughput Interaction Data Matrix Analysis

File Format

The High Throughput Interaction Data Handler allows several operations on an input file. The input file can be regarded as a data matrix. In order to be correctly analysed, the input file should have the following characteristics:

Text file, extension not important. Tipically the file will be generated by a 'save as .csv' operation in Excel or equivalent data-sheet management application

At the moment, two lines containing headers are expected. In particular, at least the second of these two lines should contain a qualifier/identifier of the respective data columns

In each line of the text file, the boundaries of the individual cells of the matrix will be marked by a specific spacer/delimiter which should be specified at the moment of file upload in the system. Accepted spacers are semicolon, comma, colon, space, tab. If you save your file in .csv format for example, the spacer will be a semicolon (';') or a comma (','), depending on the settings of your data-sheet management application.

After the first two header lines, data values should start. It is expected that the first columns of the file contain data (numeric values). Right after the data columns, a column of line qualifiers/identifiers is expected. If your lines of data correspond peptide sequences for instance, this 'identifiers' column might contain the peptide sequences or peptide unique IDs.

Some scripts of the High Throughput Interaction Data Handler, in particular Cytoscaper, at the moment also make some more specific assumptions on the format because this application was born to aid in a particular project in which the files had some more specific features.

To see an example of a valid data matrix, although small if compared to a tipical high-throughput matrix, click here

Please feel free to contact us for more information. Also look at the documentation section where more details are available

A web application written in Python by Andrea Cabibbo