HiPathia allows us to compute a signal value for each signaling path and each one of our data samples. Therefore, it allows us to compare the signal value between different conditions.

Depending on the available input data, different comparisons can be performed:

• Only expression: we can compare either two groups or correlate the path value with a continuous variable.
• Only VCF: we can compare either two groups or correlate the path value with a continuous variable.
• Expression + VCF: apart from comparing two groups and correlating the path value with a continuous variable, we can also check the effect of the mutations in the signals of each sample.

The tool can be accessed from the main menu bar, by clicking on the Differential signaling button, see Workflow for further information.

The main page of the tool is its filling in form. This form includes all the information and parameters that the tool needs to process a job. The form is divided in different panels:

• Input data
• Design data
• Species
• Parameters
• Function level analysis
• Pathways
• Job information

Once the form has been filled in, press the Launch job button to launch a job. Your job will be listed in the My jobs panel, see Workflow for further information.

The results page of the Differential signaling tool includes different output results. You can download any table or image showed in the results page by clicking on the name right before it. You can also download the pathway and function matrices by clicking on Path values, GO terms values and Uniprot keywords values respectively.

The results are divided in different panels:

• Input Parameters
• Path values
• Function based analysis
• Pathway viewer