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A Multilevel Layout Algorithm for Visualizing Physical and Genetic Interaction Networks, with Emphasis on Their Modular Organization

Johannes Tuikkala, Heidi Vähämaa, Pekka Salmela, Olli S. Nevalainen, Tero Aittokallio, A Multilevel Layout Algorithm for Visualizing Physical and Genetic Interaction Networks, with Emphasis on Their Modular Organization. Biodata Mining 5(2), , 2012.

Abstract:

Background: Graph drawing is an integral part of many systems biology studies,
enabling visual exploration and mining of large-scale biological networks. While a
number of layout algorithms are available in popular network analysis platforms, such
as Cytoscape, it remains poorly understood how well their solutions reflect the
underlying biological processes that give rise to the network connectivity structure.
Moreover, visualizations obtained using conventional layout algorithms, such as those
based on the force-directed drawing approach, may become uninformative when
applied to larger networks with dense or clustered connectivity structure.
Methods: We implemented a modified layout plug-in, named Multilevel Layout,
which applies the conventional layout algorithms within a multilevel optimization
framework to better capture the hierarchical modularity of many biological networks.
Using a wide variety of real life biological networks, we carried out a systematic
evaluation of the method in comparison with other layout algorithms in Cytoscape.
Results: The multilevel approach provided both biologically relevant and visually
pleasant layout solutions in most network types, hence complementing the layout
options available in Cytoscape. In particular, it could improve drawing of large-scale
networks of yeast genetic interactions and human physical interactions. In more
general terms, the biological evaluation framework developed here enables one to
assess the layout solutions from any existing or future graph drawing algorithm as
well as to optimize their performance for a given network type or structure.
Conclusions: By making use of the multilevel modular organization when visualizing
biological networks, together with the biological evaluation of the layout solutions,
one can generate convenient visualizations for many network biology applications.

BibTeX entry:

@ARTICLE{jTuVxSaNeAi12a,
  title = {A Multilevel Layout Algorithm for Visualizing Physical and Genetic Interaction Networks, with Emphasis on Their Modular Organization},
  author = {Tuikkala, Johannes and Vähämaa, Heidi and Salmela, Pekka and Nevalainen, Olli S. and Aittokallio, Tero},
  journal = {Biodata Mining},
  volume = {5},
  number = {2},
  pages = {   },
  year = {2012},
}

Belongs to TUCS Research Unit(s): Biomathematics Research Unit (BIOMATH)

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