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Minadakis G, Muñoz-Pomer Fuentes A, Tsouloupas G, et al. PathExNET: A tool for extracting pathway expression networks from gene expression statistics. Comput Struct Biotechnol J. 2021;19:4336-4344doi: 10.1016/j.csbj.2021.07.033.
Minadakis, G., Muñoz-Pomer Fuentes, A., Tsouloupas, G., Papatheodorou, I., & Spyrou, G. M. (2021). PathExNET: A tool for extracting pathway expression networks from gene expression statistics. Computational and structural biotechnology journal, 194336-4344. https://doi.org/10.1016/j.csbj.2021.07.033
Minadakis, George, et al. "PathExNET: A tool for extracting pathway expression networks from gene expression statistics." Computational and structural biotechnology journal vol. 19 (2021): 4336-4344. doi: https://doi.org/10.1016/j.csbj.2021.07.033
Minadakis G, Muñoz-Pomer Fuentes A, Tsouloupas G, Papatheodorou I, Spyrou GM. PathExNET: A tool for extracting pathway expression networks from gene expression statistics. Comput Struct Biotechnol J. 2021 Jul 29;19:4336-4344. doi: 10.1016/j.csbj.2021.07.033. eCollection 2021. PMID: 34429851; PMCID: PMC8363825.
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Comput Struct Biotechnol J. 2021 Jul 29;19:4336-4344. doi: 10.1016/j.csbj.2021.07.033. eCollection 2021.

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

Computational and structural biotechnology journal

George Minadakis, Alfonso Muñoz-Pomer Fuentes, George Tsouloupas, Irene Papatheodorou, George M Spyrou

Affiliations

  1. Bioinformatics Department, The Cyprus Institute of Neurology & Genetics, 6 Iroon Avenue, 2371 Ayios Dometios, Nicosia, Cyprus.
  2. The Cyprus School of Molecular Medicine, 6 Iroon Avenue, 2371 Ayios Dometios, Nicosia, Cyprus.
  3. European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK.
  4. HPC Facility, The Cyprus Institute, 20 Konstantinou Kavafi Street, 2121, Aglantzia, Nicosia, Cyprus.

PMID: 34429851 PMCID: PMC8363825 DOI: 10.1016/j.csbj.2021.07.033

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/.

© 2021 The Authors.

Keywords: Differential expression analysis; Pathway analysis; Pathway expression networks

Conflict of interest statement

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

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