RMut: R package for a Boolean sensitivity analysis against various types of mutations.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2019
2019
Historique:
received:
18
08
2018
accepted:
27
02
2019
entrez:
20
3
2019
pubmed:
20
3
2019
medline:
18
12
2019
Statut:
epublish
Résumé
There have been many in silico studies based on a Boolean network model to investigate network sensitivity against gene or interaction mutations. However, there are no proper tools to examine the network sensitivity against many different types of mutations, including user-defined ones. To address this issue, we developed RMut, which is an R package to analyze the Boolean network-based sensitivity by efficiently employing not only many well-known node-based and edgetic mutations but also novel user-defined mutations. In addition, RMut can specify the mutation area and the duration time for more precise analysis. RMut can be used to analyze large-scale networks because it is implemented in a parallel algorithm using the OpenCL library. In the first case study, we observed that the real biological networks were most sensitive to overexpression/state-flip and edge-addition/-reverse mutations among node-based and edgetic mutations, respectively. In the second case study, we showed that edgetic mutations can predict drug-targets better than node-based mutations. Finally, we examined the network sensitivity to double edge-removal mutations and found an interesting synergistic effect. Taken together, these findings indicate that RMut is a flexible R package to efficiently analyze network sensitivity to various types of mutations. RMut is available at https://github.com/csclab/RMut.
Identifiants
pubmed: 30889216
doi: 10.1371/journal.pone.0213736
pii: PONE-D-18-24401
pmc: PMC6424452
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0213736Déclaration de conflit d'intérêts
The authors have declared that no competing interests exist.
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