Research article
Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks
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* Corresponding authors: David van Dijk d.vandijk@uva.nl - Gokhan Ertaylan g.ertaylan@uva.nl
- † Equal contributors
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
BMC Systems Biology 2010, 4:96 doi:10.1186/1752-0509-4-96
Published: 15 July 2010Additional 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
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
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
Additional file 4:
Cytoscape data file of the HIV-HDF networks.
Format: PDF Size: 7.5MB Download file
This file can be viewed with: Adobe Acrobat Reader
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
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
Additional file 7:
The proteins from proteasome network and their first and second neighbors.
Format: XLSX Size: 40KB Download file
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
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
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
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
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
This file can be viewed with: Adobe Acrobat Reader
Additional file 13:
Prolog file containing the HIV-HDF regulatory network.
Format: PL Size: 1.5MB Download file
Additional file 14:
Prolog file containing the HIV-HDF activation/inhibition network.
Format: PL Size: 1.5MB Download file
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
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