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Using the clustered circular layout as an informative method for visualizing protein–protein interaction networks
Author(s) -
Fung David C. Y.,
Wilkins Marc R.,
Hart David,
Hong SeokHee
Publication year - 2010
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.201000046
Subject(s) - computer science , replication (statistics) , gene ontology , ontology , visualization , interaction network , graph layout , data mining , artificial intelligence , human–computer interaction , information retrieval , graph drawing , gene , biology , genetics , virology , philosophy , gene expression , epistemology
The force‐directed layout is commonly used in computer‐generated visualizations of protein–protein interaction networks. While it is good for providing a visual outline of the protein complexes and their interactions, it has two limitations when used as a visual analysis method. The first is poor reproducibility. Repeated running of the algorithm does not necessarily generate the same layout, therefore, demanding cognitive readaptation on the investigator's part. The second limitation is that it does not explicitly display complementary biological information, e.g. Gene Ontology, other than the protein names or gene symbols. Here, we present an alternative layout called the clustered circular layout. Using the human DNA replication protein–protein interaction network as a case study, we compared the two network layouts for their merits and limitations in supporting visual analysis.