PathExNET: A tool for extracting pathway expression networks from gene expression statistics

Abstract

A fundamental issue related to the understanding of the molecular mechanisms, is the way in which common pathways act across different biological experiments related to complex diseases. Using network-based approaches, this work aims to provide a numeric characterization of pathways across different biological experiments, in the prospect to create unique footprints that may characterise a specific disease under study at a pathway network level. In this line we propose PathExNET, a web service that allows the creation of pathway-to-pathway expression networks that hold the over- and under expression information obtained from differential gene expression analyses. The unique numeric characterization of pathway expression status related to a specific biological experiment (or disease), as well as the creation of diverse combination of pathway networks generated by PathExNET, 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. PathExNET is available at: https://bioinformatics.cing.ac.cy/PathExNET and at https://pathexnet.cing-big.hpcf.cyi.ac.cy/

Network-Based Analysis Identifies Targetable Pathways in Comorbid Type II Diabetes and Neuropsychiatric Disorders

“…Finally, we devised the ‘minimum path to comorbidity’ algorithm that allowed us to identify the shortest path that might facilitate the development of comorbid DM2 and NPDs. Existing tools utilizing different methods allow for the recreation, visualization, and analysis of pathway-to-pathway networks, such as ComPath (91), ClueGO (43), PANEV (92) and PathExNET (93). While some of these tools allow to introduce complementary pathways to create a fully connected network (94), our approach allows for the introduction of specific pathways into the network that act as disease reference points, making them relevant to the diseases under investigation.…”

PathIN: an integrated tool for the visualization of pathway interaction networks

“…Casting biological pathways as networks has become a promising and valuable Systems Bioinformatics approach that aims to enhance post-experimental omics analyses and to provide further insights on the functional inter-relation of pathways [16] , [17] , [37] . The powerful concept of the graph theory and the plurality of pathway-based information included in eminent database repositories such as the KEGG [9] , the Reactome [10] and the Wiki Pathways [11] , has put significant contribution to the understanding and development of novel software that allows the integration of pathway data at network level [43] , [44] .…”

“…Eminent tools that involve pathway network visualisation such as ClueGO [36] , PathExNET [37] , PathME [38] , PANEV [39] , ComPath [40] , and many other [41] , [42] , can successfully create pathway-to-pathway networks. However, although these applications are based on the connectivity information provided by the available pathway repositories, the commonality numeric information draws only from the genes involved in the pathways.…”

Genome Scale Pathway-Pathway Co-functional Synergistic Network (PcFSN) in Oryza Sativa

“…miRNA mediated gene regulatory network in roots, signal transduction, leaf senescence, vegetative and reproductive regulation are few examples [3][4][5][6]. Recently pathway centric co-expression studies are also gaining importance so that gap between gene expression and pathway perturbation can be minimised [7,8]. While these studies have shed light on condition and tissue specific regulatory role of miRNAs in other species, a comprehensive analysis of genome scale pathway-mediated co-target and co-functional networks in rice has not been done so far.…”