Welcome to our wiki page: ''How to visually interpret biological data using networks''

From this page you can learn more about the different datasets used to build the network shown in Figure 1b of the Primer about network visualization [Merico, D. Gfeller, D. & Bader, G.D., Nat. Biotech. x, x (2009), PDF] and download them if you want to try visualizing and analyzing them with your own tools.

  1. How to visually interpret biological data using networks
    Merico D, Gfeller D, Bader GD
    Nature Biotechnology 2009 Oct 27, 921-924
    PubMed Abstract - PDF

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Figure 1: Network visualization of chromosome maintenance and duplication machinery in baker’s yeast, Saccharomyces cerevisiae (yeast_duplication_network.pdf).

Figure description

Nodes represent proteins that are annotated as being located on the chromosome by the Gene Ontology project (for clarity, the suffix ‘p’ has been removed from yeast protein names). Node colors specify chromosomal location sub-categories: replication fork, red; nucleosome, green; kinetochore, blue; and other chromosome components, yellow. Edges represent protein-protein interactions that were manually extracted from publications by BioGRID database curators. Gene expression data of cells monitored during one round of the cell cycle are visually annotated on the network. Edge width encodes positive Pearson correlation between transcript profiles. Node size corresponds to the transcriptional amplitude, which is a measure of how much expression changes over the cell cycle. The network was visualized using the Cytoscape software.


The datasets described below can be freely downloaded. They have been formatted to be readily usable with Cytoscape software.

Visualizing the network using Cytoscape

  1. Download all the files listed above and make sure you have Cytoscape installed and running smoothly.
  2. Open Cytoscape.
  3. Go to File/Import/network(multiple file types) and select "protein_protein_interaction.sif".
  4. Go to File/Import/Node Attributes and select "GO_annotation.txt".
  5. Go to File/Import/Node Attributes and select "yeast_gene_names.txt".
  6. Go to File/Import/Node Attributes and select "gene_expression_amplitude.txt".
  7. Go to File/Import/Edge Attributes and select "gene_expression_correlation.txt".
  8. To layout the network, go to Layout/Cytoscape Layouts/Force-directed Layouts/unweighted. You can try other layouts as well.
  9. Go to View/Show Graphics Details to see the original gene names.
  10. To add colors to the nodes, click on VizMapperTM button (you may need to click on the right arrow after the network button). In the Visual Mapping Browser double click "Node Color". Please select a value! appears on the right column: select "GO annotation". Please select a mapping!: choose "Discrete Mapping". For each GO category, you can now choose the color you want.
  11. To display the standard protein names as node labels, double click "Node Label". Select "Yeast gene names" and choose "Passthrough Mapping".
  12. To change the size of the nodes according to their gene expression amplitude, double click on "Node Size". Select "Gene expression amplitude". Choose "Continuous Mapping". Clicking on the chart that appears, you can now choose what node size you wish for the different amplitude values.
  13. To change the width of the edges according to the gene expression correlation, double click on Edge Size. Select "Gene expression correlation" and choose "Continuous Mapping". You can now choose what edge width you wish for the different correlation values.

Many other options to improve the layout or add other kind of visual attributes are available within Cytoscape. Have fun playing with them!

NetworkPrimerNBT (last edited 2020-08-16 04:11:59 by GaryBader)

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