What is GFD-Net

GFD-Net is a Cytoscape app designed to visualize and analyze the functional dissimilarity of gene networks. GFD-Net can analyze a gene network based on Gene Ontology (GO) and calculate a quantitative measure of its functional dissimilarity, i.e. a quantitative value of the degree of dissimilarity between the connected genes in it.

After the analysis, users can visualize the information retrieved from GO.


What is it useful for

GFD-Net provides researchers with an easy way to validate their inferred networks and find out in which way the genes in a network are related to each other. Such information helps finding high functionally related subsets as well as the concrete function of a specific gene in a given network

How does it work

GFD-Net is based on an adaptation of the GFD approach presented in Díaz Díaz and Aguilar Ruiz, 2011 which uses the prior biological knowledge contained in GO to establish the quality of of gene sets. In this type of measure, it is considered that absolutely all the genes are related to each other disregarding the possibly that some of them may be related while others may be not. On the other hand, GFD-Net assumes that all the genes on the same network are involved in the same biological process. This means that these genes may have different functions, but they have been put together on the same network because they are somehow related in a biological sense (Biological Process, Molecular Function, Cellular Component) and takes into account only the genes directly related to each other i.e. connected by an edge.

The analysis is performed in four steps (click on them to read more):

It should be taken into consideration that GFD-Net is oriented to connected networks where most of the genes are contained in the ontology being used. This is because all the genes that cannot be found are removed from the network and the dissimilarity between disconnected nodes is not calculated. The more genes that are removed or pairs that are disconnected, the less reliable the results will be.

How to use it

All the information about installation and use of GFD-Net can be found in the User Manual using the Downlaod button or clicking here


Díaz-Montaña, Juan J., Norberto Díaz-Díaz, and Francisco Gómez-Vela. "GFD-Net: a novel semantic similarity methodology for the analysis of gene networks." Journal of Biomedical Informatics (2017).
(Use this paper to reference GFD-Net)

Diaz-Montana, Juan J., and Norberto Diaz-Diaz. "Development and use of the Cytoscape app GFD-Net for measuring semantic dissimilarity of gene networks." F1000Research 3 (2014).

Authors and Contributors

Support or Contact

In case of having any trouble with the app, check out the User Manual. If your problem is not solved you can contact jjdiamon@alumno.upo.es and we'll try to help you as soon as possible.