Spatial Analysis of Functional Enrichment (SAFE) in Large Biological Networks.
Methods Mol Biol
; 1819: 249-268, 2018.
Article
in En
| MEDLINE
| ID: mdl-30421408
Spatial analysis of functional enrichment (SAFE) is a systematic quantitative approach for annotating large biological networks. SAFE detects network regions that are statistically overrepresented for functional groups or quantitative phenotypes of interest, and provides an intuitive visual representation of their relative positioning within the network. In doing so, SAFE determines which functions cocluster in a network, which parts of the network they are associated with and how they are potentially related to one another.Here, I provide a detailed stepwise description of how to perform a SAFE analysis. As an example, I use SAFE to annotate the genome-scale genetic interaction similarity network from Saccharomyces cerevisiae with Gene Ontology (GO) biological process terms. In addition, I show how integrating GO with chemical genomic data in SAFE can recapitulate known modes of action of chemical compounds and potentially identify novel drug mechanisms.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Saccharomyces cerevisiae
/
Gene Regulatory Networks
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Molecular Sequence Annotation
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Gene Ontology
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Models, Biological
Language:
En
Journal:
Methods Mol Biol
Journal subject:
BIOLOGIA MOLECULAR
Year:
2018
Document type:
Article
Affiliation country:
Estados Unidos
Country of publication:
Estados Unidos