PathExNET is a tool for extracting pathway-expression networks from differential gene expression analyses

PathExNET is a web service that allows the creation of pathway expression networks that hold the over- and under-expression information obtained from differential gene expression analyses. PathExNET holds a large database of reference pathway-to-pathway networks, which have been developed through the freely available information included in the KEGG, Reactome and Wiki Pathways database repositories. Users can upload their differential gene expression statistical analysis, followed with pathways and/or genes of interest, and further chose a score methodology to create and explore the derived pathway-to-pathway expression networks. In order to provide a concrete set of well-evaluated differential gene expression statistical analyses and to further increase the data-availability and easy data access of PathExNET, an additional tool has been rooted in PathExNET framework that allows to search and directly import, pre-processed statistic files from the Expression Atlas (EA) ( data repository of the European Bioinformatics Institute (EMBL-EBI) ( Depending on the input type PathExNET provides:

  • pathway-to-pathway expression networks where the node size represents a specific score and the edge size represents the number of common genes between two pathways
  •  pathway-to-gene networks where the edges characterise the relation between pathway and gene.
  •  A series of pathway expression scores related to the over- and under-expression statistical information of genes
  •  Network based information on a single pathway and it's first neighbours
  •  Further statistical information on User's input

PathExNET comes with a frontend web interface that consists of the mainframe and a help page, written in HTML, PHP and JavaScript language environments. The mainframe provides 2 individual steps designed to guide the user until the end of the workflow process. The backend of PathExNET has been written in R environment, where several functionalities have been parallelised to achieve fast performance. Evaluation, testing and understanding of PathExNET functionalities can be easily performed by means of several available example datasets provided on the web site.

The underlying web service, is expected to provide a concrete contribution towards the individualization of disease, and further lead to a more precise personalised medicine and management of treatment.

Resource organization

Resource providers

The Cyprus Institute of Neurology and Genetics

Iroon Avenue 6, Agios Dometios, 2371 Nicosia, Cyprus (CY)

The Cyprus Institute of Neurology and Genetics

Iroon Avenue 6, Agios Dometios, 2371 Nicosia, Cyprus (CY)







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Target users

Research Groups Research Managers Innovators Students Research Projects Researchers Research Infrastructure Managers Research Organisations Research Networks Research Communities

Access type

Remote Virtual

Access mode



Pathway expression networks Differential expression analysis Pathway analysis


George Spyrou, Head of the Bioinformatics Department
phone: +35722358600

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The NI4OS-Europe project is funded by the European Commission under the Horizon 2020 European research infrastructures grant agreement no. 857645.