HiPathia is a web tool for the interpretation of the consequences of the combined changes of gene expression levels and/or genomic mutations in the context of signalling pathways. HiPathia transforms uninformative gene expression and/or genomic variation data into signaling circuit activities, which carry information on the different cell functionalities triggered by them. Such signaling activities not only account for the underlying molecular mechanisms of diseases or the mode of action of drugs but they can also be used to interpret the effect of mutations or gene expression perturbations.

Along this tutorial you will learn how to use the HiPathia pathway suite and find different worked examples.

The HiPathia web server integrates four different pathway analysis modules:

• Differential signaling provides an estimation of significant cell signaling activity changes across different conditions.
• Prediction allows you to train a prediction test and test it with different data.
• Perturbation effect is an interactive working environment to simulate the effect of different interventions (e.g. knock-out, over-expression, drugs, etc.) over the activity of signaling circuits in the pathways, as well as their potential functional consequences in the cell.
• Variant interpreter provides an estimation on the potential impact of genomic variation on cell signaling and ultimately on cell functionality.