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Topological analysis and interactive visualization of biological networks and protein structures

Nature Protocols volume 7, pages 670–685 (2012)Cite this article

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Abstract

Computational analysis and interactive visualization of biological networks and protein structures are common tasks for gaining insight into biological processes. This protocol describes three workflows based on the NetworkAnalyzer and RINalyzer plug-ins for Cytoscape, a popular software platform for networks. NetworkAnalyzer has become a standard Cytoscape tool for comprehensive network topology analysis. In addition, RINalyzer provides methods for exploring residue interaction networks derived from protein structures. The first workflow uses NetworkAnalyzer to perform a topological analysis of biological networks. The second workflow applies RINalyzer to study protein structure and function and to compute network centrality measures. The third workflow combines NetworkAnalyzer and RINalyzer to compare residue networks. The full protocol can be completed in ∼2 h.

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Figure 1: Outline of the protocol.
Figure 2: Screenshot of network statistics computed by NetworkAnalyzer.
Figure 3: Simultaneous view of RIN and 3D protein structure by RINalyzer.
Figure 4: Comparison network generated by RINalyzer.

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Acknowledgements

We thank D. Buezas, T. Kacprowski and C. Weichenberger for their useful comments on the workflows and the manuscript. This study was partially funded by the BMBF through the German National Genome Research Network (NGFN) and the Greifswald Approach to Individualized Medicine (GANI_MED). It was also conducted in the context of the DFG-funded Cluster of Excellence for Multimodal Computing and Interaction.

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Authors and Affiliations

  1. Max Planck Institute for Informatics, Saarbrücken, Germany

    Nadezhda T Doncheva, Yassen Assenov & Mario Albrecht

  2. Center for Biomedicine, EURAC research, Bolzano, Italy

    Francisco S Domingues

  3. Institute of Biometrics and Medical Informatics, University Medicine Greifswald, Greifswald, Germany

    Mario Albrecht

Authors
  1. Nadezhda T Doncheva
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  2. Yassen Assenov
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  3. Francisco S Domingues
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  4. Mario Albrecht
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Contributions

N.T.D. conceived and drafted the workflows. Y.A. contributed to the workflows. N.T.D., Y.A., F.S.D. and M.A. wrote and approved the manuscript.

Corresponding author

Correspondence to Mario Albrecht.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Figures

Supplementary Figure 1 | Results dialog of NetworkAnalyzer The first tab of this dialog shows the computed simple network parameters. The other tabs display complex network parameters as histograms or scatter plots. The complete set of topological parameters is referred to as network statistics. These statistics can be saved to and reloaded from a text file to avoid recomputation. The topological parameters that are computed for each node or edge, e.g., node degree, neighborhood connectivity, and betweenness, can be visualized in the network view. (PDF 1921 kb)

Supplementary Figure 2 | Mapping topological parameters to the network view In the PPI network from Yu et al. (Nat Methods, 8:478–480, 2011), the node degree and clustering coefficient are mapped to node size and node color, respectively. Nodes of low degree appear as small circles, whereas nodes of high degree are enlarged. Additionally, nodes with low clustering n green, and nodes with high clustering coefficient in red.

Supplementary Figure 3 | Visual Properties dialog of RINalyzer RINalyzer provides a user-friendly interface for customizing the network view of RINs in Cytoscape. The visual properties are arranged in two main groups: general and node properties (left), and edge properties (right). For instance, the user can color nodes according to secondary structure, adjust the style of node labels, or select the colors of the different edge interaction types. The default values of the visual properties can be restored at any time; a new set of values can also be defined as default.

Supplementary Figure 4 | Backbone representation of the HIV-1 protease structure and the corresponding RIN The RIN of the HIV-1 protease (PDB identifier 1HIV) is displayed by RINalyzer in Cytoscape (top right), and the backbone representation of the corresponding 3D structure is shown in UCSF Chimera (bottom right). RIN nodes and protein residues are colored according to secondary structure: blue for helices and red for strands. In the network view of the RIN, all non-covalent interaction edges are hidden by using the RIN Visual Properties dialog (left) so that only the backbone edges are visible. This screenshot is taken after finishing Step 2B(v) of the protocol.

Supplementary Figure 5 | Node Sets interface of RINalyzer This user interface offers four menus to create, load, save, and modify sets of residue nodes (left). It also supports typical set operations such as union and intersection RINalyzer keeps track of all operations performed with each node set (left bottom). The nodes in the network view of the RIN for the HIV-1 protease (top right) and the residues in the corresponding 3D protein structure (bottom right) are colored according to the node set they belong to: light blue for Chain A; dark blue for Chain A Interface; orange for Chain B; red for Chain B Interface; and pink for Chain I. The node set Chain A Interface is a subset of Chain A. This screenshot is taken after finishing Step 2B(ix) of the protocol.

Supplementary Figure 6 | Centrality Analysis Settings of RINalyzer This dialog allows customizing a number of settings for the network centrality analysis (see Box 3 for a detailed description).

Supplementary Figure 7 | Centrality analysis results by RINalyzer The panel RINalyzer Centralities consists of different sections. The first section contains general analysis information and allows the user to show all computed centrality values in a table or to save them to a file. The other sections provide access to the values of each centrality measure. In particular, the user can apply a selection filter to select nodes with centrality values in a given range, view the values in a table, or save them to a file. This figure shows the results of the centrality analysis performed in Step 2B(xii) and explored in Steps 2B(xiii) and (xiv)

Supplementary Figure 8 | Overview of batch analysis using NetworkAnalyzer The user can perform automatized batch analysis of multiple networks. First, the user has to select an input and output directory for the batch analysis (a). Afterwards, NetworkAnalyzer performs an automatic analysis and informs about the computation progress (b). Finally, the batch analysis results are presented in a dialog that lists each loaded network with its edge interpretation and the resulting network statistics file (c).

Supplementary Figure 9 | Network statistics of the four subunits of human deoxyhaemoglobin The batch analysis results dialog allows users to open the network statistics of the analyzed networks. The computed simple topological parameters for the networks representing all subunits of the human deoxyhaemoglobin are displayed as follows: chain A (top left), chain B (top right), chain C (bottom left), and chain D (bottom right).

Supplementary Figure 10 | Simplified view of a comparison network generated by RINalyzer Edge line styles correspond to non-covalent residue interactions (edge type combi:all_all) that are preserved in both subunits (black solid lines), present only in the α subunit (green dashed lines) or only in the β subunit (red dotted lines). RIN nodes that represent aligned residues are pink, whereas nodes that correspond to unaligned residues are either green (α subunit only) or red (β subunit only). This screenshot is taken after finishing Step 2C(v) of the protocol.

Supplementary Data 1

This file is in the simple interaction format (SIF) and contains the protein-protein interactions from Yu et al. (Nat Methods, 8:478–480, 2011). (TXT 17 kb)

Supplementary Data 2

This data file contains four RINs that represent the four subunits of human deoxyhaemoglobin (chains A, B, C, and D in the PDB structure with identifier 4HHB). The RINs were generated using the RINerator package (http://rinalyzer.de/rinerator.php). (ZIP 29 kb)

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Doncheva, N., Assenov, Y., Domingues, F. et al. Topological analysis and interactive visualization of biological networks and protein structures. Nat Protoc 7, 670–685 (2012). https://doi.org/10.1038/nprot.2012.004

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