Results: 5

1.
Figure 2

Figure 2. From: GPS-Prot: A web-based visualization platform for integrating host-pathogen interaction data.

GPS-Prot: a web-based platform for visualizing diverse HIV-host data. (A) GPS-Prot homepage. Searches are initiated by selecting databases and an HIV or host protein. (B) A Touchgraph Navigator window is launched to display results of a search, which contains the protein interaction network. Single clicking any interaction ("edge", or gray line connecting proteins) provides the evidence from the literature for that interaction in the left-hand panel. Clicking on any protein in the diagram ("node") pulls up details for that protein (e.g. panel labeled CUL5). There is also a searchable table that can be sorted by score, database or experiment. A new network can be created by double clicking any protein (node), thus, it is possible to "walk through" the entire HIV-human or human-human interactome.

Marie E Fahey, et al. BMC Bioinformatics. 2011;12:298-298.
2.
Figure 1

Figure 1. From: GPS-Prot: A web-based visualization platform for integrating host-pathogen interaction data.

Numerous host factors have been identified for HIV by small-scale and high-throughput experiments, with little overlap between the various sources. (A) Venn diagram shows overlap from four HIV-based genetic screens [14-17]. Only three intersections show a significantly higher number of shared genes than expected, which are highlighted in large type. Ten genes are shared between the Brass and König datasets (p = 0.01), 11 between Brass and Zhou datasets (p = 0.0014), and three between Brass, König, and Zhou datasets (p = 5 × 10-5). None are shared between all four datasets. (B) Venn diagram shows a similar analysis for three HIV-dependent proteomic profiling screens [26-28]. Large type highlights statistically significant overlaps between the datasets (below 1 × 10-4).

Marie E Fahey, et al. BMC Bioinformatics. 2011;12:298-298.
3.
Figure 3

Figure 3. From: GPS-Prot: A web-based visualization platform for integrating host-pathogen interaction data.

Viral RNAi screens are enriched for host factors that are subunits of human complexes. (A) All viral RNAi screens identify significantly more human complex subunits identified than expected (HIV 23%, influenza 25%, and hepatitis C 24%), compared to the number of proteins in the human genome assigned to complexes by CORUM (12%). P values shown are based on the hypergeometric distribution. We find no strong enrichment of protein complexes in a screen of Mtb host factors (13%). (B) Network of Vif interactors from GPS-Prot using the optional NIAID HIV-1-human interactions database, instead of VirusMINT. Including CORUM as a database brings complex subunits closer together in the network, for example the cluster of proteasome complex subunits shown to the lower left (e.g. PSMA, PSMB, PSMC, etc).

Marie E Fahey, et al. BMC Bioinformatics. 2011;12:298-298.
4.
Figure 5

Figure 5. From: GPS-Prot: A web-based visualization platform for integrating host-pathogen interaction data.

User-generated data can be uploaded and viewed in the context of complete PPI networks from public databases. (A) Vif network from GPS-Prot, including an uploaded dataset from AP-MS experiments (red-tagged nodes). Huwe1 is among several proteins in the uploaded dataset (Jager et al., submitted) that are not found in other databases (e.g., not present in Figure 2B), and were also previously identified by genetic/proteomic screens. (B) HIV Vif interacts with endogenous HUWE1 in 293 cells. 3xFLAG-tagged Vif, Vpr, and Nef were immunoprecipitated with anti-FLAG agarose beads. Lysates (L), remaining supernatant (S) and eluates (E) were analyzed by SDS-PAGE and Western blotting with antibodies as indicated. The same band is identified in the Vif pulldown by antibodies against the known CUL5 E3 ligase complex, anti-CUL5 (not shown) and anti-ELOB (TCEB2) as well as anti-Huwe1 antibodies, but not by the control anti-UPF1 antibody.

Marie E Fahey, et al. BMC Bioinformatics. 2011;12:298-298.
5.
Figure 4

Figure 4. From: GPS-Prot: A web-based visualization platform for integrating host-pathogen interaction data.

Five complexes implicated in HIV pathogenesis by analysis with CORUM. (A) Network analysis of RNAi datasets. Gray nodes are subunits present in the complex according to the CORUM database. Colored subunits (nodes) were reported in one or more of the genetic screens. Based on the hypergeometric distribution, we find significantly more subunits of the proteasome (p = 4.2 × 10-9), Mediator (p = 1.1 × 10-9), and the exosome (p = 2.1 × 10-3) than expected. Subunits of ESCRT III and CCT complexes are not significantly enriched. The table shows the number of complexes and subunits identified by two, three or four RNAi screens. As with genetic screens, there is greater overlap between datasets when analyzed in terms of subunits of complexes as opposed to isolated proteins. (B) Network analysis of proteomic profiling datasets. The same complexes are shown as in panel A, with subunits highlighted as they occur in different datasets. Mediator and exosome complexes are not covered more than expected, but significantly more subunits than expected are found for ESCRT III (p = 8.4 × 10-3) and CCT complexes (p = 2.0 × 10-7). The proteasome is the only complex where more subunits than expected are identified by both genetic and proteomic profiling screens (p = 7.0 × 10-23).

Marie E Fahey, et al. BMC Bioinformatics. 2011;12:298-298.

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