Supplementary Data for "The Global Landscape of Human Proteins Targeted by Viruses and Other Pathogens"




Authors:

Matthew D. Dyer, T. M. Murali, and Bruno W. Sobral


Citation:

PLos Pathogens (In press)


Description:

Infectious diseases result in millions of deaths each year. Mechanisms of infection have been studied in detail for many pathogens. However, many questions are relatively unexplored. What are the properties of human proteins that interact with pathogens? Do pathogens interact with certain functional classes of human proteins? Which infection mechanisms and pathways are commonly triggered by multiple pathogens? In this paper, we provide the first study of the landscape of human proteins interacting with pathogens. We integrate human-pathogen protein-protein interactions (PPIs) for 190 pathogen strains from seven public databases. Nearly all of the 10,477 human-pathogen PPIs are for viral systems (98.3%), with the majority belonging to the human-HIV system (77.9%). We find that both viral and bacterial pathogens tend to interact with hubs (proteins with many interacting partners) and bottlenecks (proteins that are central to many paths in the network) in the human PPI network. We construct separate sets of human proteins interacting with bacterial pathogens, viral pathogens, and those interacting with multiple bacteria and with multiple viruses. Gene Ontology functions enriched in these sets reveal a number of processes, such as cell cycle regulation, nuclear transport, and immune response, that participate in interactions with different pathogens. Our results provide the first global view of strategies used by pathogens to subvert human cellular processes and infect human cells.


Data:

File Description Links
Enriched
Gene
Ontology
Functions
Enriched Gene Ontology functions in 58 sets of human proteins: those interacting with each of the 54 pathogen groups, those interacting with at least one and multiple bacterial pathogens (labelled "Bacteria" and "Multibacteria"), and those interacting with at least one and multiple viral pathogens (label "Virus" and "Multivirus"). The background is the set of all human proteins that interact with at least one other human protein. Results are available as tab-delimited files or as html pages containing images of the networks spanning the proteins with the enriched function. We only display functions enriched with a p-value at most 0.05. Text
Html
Enriched Gene Ontology functions in 58 sets of human proteins: those interacting with each of the 54 pathogen groups, those interacting with at least one and multiple bacterial pathogens (labelled "Bacteria" and "Multibacteria"), and those interacting with at least one and multiple viral pathogens (label "Virus" and "Multivirus"). The background is the set of all human proteins interacting with at least one pathogen group. Results are available as tab-delimited files or as html pages containing images of the networks spanning the proteins with the enriched function. We only display functions enriched with a p-value at most 0.05. Text
Html
Other
files
Tab-delimited file containing all the host-pathogen protein-protein interactions used in this study. The format is human UniProt id, pathogen UniProt id, pubmed id, experimental method, and source. Text
Tab-delimited of computed biclusters of enriched functions among the 54 pathogen groups using the background of all human proteins that interact with at least one other human protein. The format is the identifier which contains the bicluster number, the number of pathogen groups, and the number of enriched functions, followed by the list of pathogen groups and enriched functions. Text
Tab-delimited file of degree, centrality, number of pathogen interactors, and the most specific annotations within each of the three GO hierarchies for each human protein that interact with at least one pathogen protein. We provide this data for researchers interested in prioritizing anti-viral and anti-bacterial targets. Text