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Open Access Highly Accessed Research article

Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks

David van Dijk1*, Gokhan Ertaylan1*, Charles AB Boucher2 and Peter MA Sloot1

Author Affiliations

1 Computational Science, University of Amsterdam, Sciencepark 107, 1098 XG Amsterdam, The Netherlands

2 Department of Virology, Erasmus Medical Center, 's-Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands

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BMC Systems Biology 2010, 4:96  doi:10.1186/1752-0509-4-96

Published: 15 July 2010

Additional files

Additional file 1:

Protein interaction network of HIV proteins and HDFs. Intended to be opened in IGraph or any other graph analysis software that supports GML files.

Format: GML Size: 2.7MB Download file

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Additional file 2:

Protein interaction network of HDFs and non-HDF human proteins. Intended to be opened in IGraph or any other graph analysis software that supports GML files.

Format: GML Size: 12.1MB Download file

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Additional file 3:

High resolution picture of the HIV-HDF network generated with Cytoscape, in spring embedded layout.

Format: PDF Size: 9KB Download file

This file can be viewed with: Adobe Acrobat Reader

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Additional file 4:

Cytoscape data file of the HIV-HDF networks.

Format: PDF Size: 7.5MB Download file

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Additional file 5:

HIV-human connectivities for regulatory, activation/inhibition and binds interactions. A: Number of HIV-human interactions for each HIV protein, B: Normalized relative number of HIV-human interactions for each HIV protein. The y-axis enumerates the n-fold representation of interactions per HIV protein divided by the relative number of interactions of the respective protein in the total network. An n-fold representation of n > 1 shows an over-representation, whereas n < 1 signifies an under-representation.

Format: ZIP Size: 2.2MB Download file

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Additional file 6:

Spreadsheet document with all the proteins from the network centrality analysis.

Format: XLS Size: 1.1MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 7:

The proteins from proteasome network and their first and second neighbors.

Format: XLSX Size: 40KB Download file

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Additional file 8:

High resolution image of the proteasomal network generated with Cytoscape, in spring embedded layout.

Format: PDF Size: 1.1MB Download file

This file can be viewed with: Adobe Acrobat Reader

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Additional file 9:

Heat-map image from proteasomal network to annotate for the common GeneOntology terms associated with cell cycle in cluster-2.

Format: TIFF Size: 2MB Download file

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Additional file 10:

Heat-map image from proteasomal network to annotate for the common GeneOntology terms associated with regulation in cluster-2.

Format: TIFF Size: 2.7MB Download file

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Additional file 11:

Heat-map image from proteasomal network to annotate for the common GeneOntology terms in cluster-3.

Format: TIFF Size: 2.2MB Download file

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Additional file 12:

Tables of all found significantly over-represented network motifs in the regulatory and activation/inhibition sub-networks. Also included are tables of specific protein involvement and Gene Ontology analysis of the motifs.

Format: PDF Size: 792KB Download file

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Additional file 13:

Prolog file containing the HIV-HDF regulatory network.

Format: PL Size: 1.5MB Download file

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Additional file 14:

Prolog file containing the HIV-HDF activation/inhibition network.

Format: PL Size: 1.5MB Download file

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Additional file 15:

Prolog script with an implementation of the motif detection and network randomization algorithm for the regulatory network.

Format: PL Size: 41KB Download file

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Additional file 16:

Prolog script with an implementation of the motif detection and network randomization algorithm for the activation/inhibition network.

Format: PL Size: 30KB Download file

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