PathWalks: identifying pathway communities using a disease-related map of integrated information.
Journal
Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944
Informations de publication
Date de publication:
01 07 2020
01 07 2020
Historique:
received:
05
02
2020
revised:
11
04
2020
accepted:
27
04
2020
pubmed:
6
5
2020
medline:
29
12
2020
entrez:
6
5
2020
Statut:
ppublish
Résumé
Understanding the underlying biological mechanisms and respective interactions of a disease remains an elusive, time consuming and costly task. Computational methodologies that propose pathway/mechanism communities and reveal respective relationships can be of great value as they can help expedite the process of identifying how perturbations in a single pathway can affect other pathways. We present a random-walks-based methodology called PathWalks, where a walker crosses a pathway-to-pathway network under the guidance of a disease-related map. The latter is a gene network that we construct by integrating multi-source information regarding a specific disease. The most frequent trajectories highlight communities of pathways that are expected to be strongly related to the disease under study.We apply the PathWalks methodology on Alzheimer's disease and idiopathic pulmonary fibrosis and establish that it can highlight pathways that are also identified by other pathway analysis tools as well as are backed through bibliographic references. More importantly, PathWalks produces additional new pathways that are functionally connected with those already established, giving insight for further experimentation. https://github.com/vagkaratzas/PathWalks. Supplementary data are available at Bioinformatics online.
Identifiants
pubmed: 32369599
pii: 5830272
doi: 10.1093/bioinformatics/btaa291
pmc: PMC7332569
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4070-4079Informations de copyright
© The Author(s) 2020. Published by Oxford University Press.
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