Filling in a tool form

HiPathia integrates two different pathway tools: Differential signaling and Prediction. Both pathway tools can be accessed from the main menu bar, by clicking on their respective names (see Workflow).

The main page of a pathway 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
• Pathways
• Job information

In the input data panel, we must introduce the expression data and, optionally, the variant data.

The expression data can be either an:

• Expression matrix provided by yourself (see how to upload files in Upload your data), or
• Expression vector taken from an expression database. In this case, we must choose the tissue database and tissue names.

The variant data must be a VCF file.

The design data panel allows you to choose the kind of experiment you want to perform. You can choose between two main experimental designs:

• Two group comparison:
• Correlation with continuous variable: