Table 1. Classification of MPD proteins. Source All Organisms Mus musculus (Mouse) Toxoplasma gondii Bacillus anthracis Vibrio cholerae Homo sapiens (Human) Salmonella typhimurium Salmonella typhi Brucella abortus Cryptosporidium parvum Vaccinia virus Monkeypox virus Francisella tularensis Yersinia pestis Human SARS virus Mass Spec Data Microarray Data Interaction Data New Structures, (Domains) Sequenced Clones Uncharacterized Proteins Proteins in Pathways Classified in Families With GO Terms Protein Count 35,112 7,823 6,678 5,854 3,732 3,526 3,406 2,061 944 609 161 130 62 75 6 25,289 7,031 1,363 6 (15) 9,074 10,637 9,988 24,953 22,265 18,165 583 With Bioinformatics Resource Center Links With Immune Epitope DB links The content of the MPD as of July 2009. Numbers represent the total number of proteins that meet the listed criteria, for example, have one or more GO term or pathway or link associated with the protein. doi:10.1371/journal.pone.0007162.t001 (Unigene, RefSeq, IPI, nr) were reported in the research results that all represent either the gene or protein sequence for this single mouse protein. 2) Discovery of additional experimental informa- tion from other studies. Fifteen of the sixteen proteins found in the query also have mass spec data from Caprion Proteomics, as indicated in the ‘experiment’ column by Caprion_05, 06 and _10. Caprion is studying Brucella abortus and using a similar mouse macrophage model. Currently, only the data for uninfected macrophages is available from Caprion. Additional data on Brucella and mouse proteins from bacterial infected macrophages should be included in future releases. From the results display, one can follow links to view the iProClass protein report with executive summaries of the results from the PRCs and information collected from over 100 public resources or drill down to view the specific peptides or expression values seen in these studies, read publications and methods about the experiments or download the data for additional analysis. With a comprehensive protein data warehouse, one can also broaden the search for relevant data and information from related organisms using protein cluster or family information. In Figure 4 we illustrate this by selecting one protein, K1033_MOUSE, an uncharacterized protein seen in three datasets from infected mouse macrophages. Using the UniRef90 cluster ID [22] to query for all Pathogen-Host Omics Data proteins with at least 90% identity and no gaps, we find the human homolog K1033_HUMAN was detected in HeLa cells infected with vaccinia and monkypox virus. If we do a batch retrieval using Uniref90 IDs from all 16 original mouse proteins, we find 12 human homologs were also detected in studies of orthopox infection (not shown). The identification of a hypothetical protein with differential gene and protein expressions in two host systems (mouse macrophage and HeLa cells) infected by different bacterial (Bacillus anthracis and Salmonella typhimurium) and viral (orthopox) pathogens suggest that this protein should be prioritized for additional analysis and functional characterization. Example II: Combining data from different studies. Discovering and comparing experimental results across laboratories and data types can help lead to new hypotheses for further experimentation [23,24,25]. Although different laboratories use different sample preparation, detection and analysis techniques making some direct comparisons difficult, having the data together in one place allows queries and comparisons between proteins and gene sets to be combined and additional analysis undertaken. In this example, data from different labs and data types are combined for further analysis. A query of the MPD on data type = ‘‘interaction’’ AND organism name = ‘‘virus’’ finds 33 vaccinia virus proteins with interactions with human proteins determined by Myriad Genetics. Browsing the results display shows that 25 of the proteins were also seen in mass spec work published by PNNL [26]. By combining the two experimental data sets Experiment = ‘‘MYRIAD_05’’ AND ‘‘PNNL_MS_09’’, we find 83 virus and human proteins with both mass spec and interaction data from each laboratory. Further investigation into the experimental details shows that a protein interaction network was determined by Myriad Genetics using a yeast-two hybrid assay to screen viral bait proteins against a library of human prey proteins cloned from different tissues. The mass spec data from PNNL was obtained from viral preparations isolated from infected human HeLa cells. The work from PNNL contained quantitative information in the form of spectral counts and Accurate Mass Tag [27] intensities, downloadable from the project FTP site. We combined all the vaccinia plus human interaction data with peptide counts for each protein and visualized the results using Cytoscape [28,29]. The complete network of results is shown in Figure 5A. Various methods have been tried and compared for filtering large intra-species interaction networks to limit false positives and to select the biologically relevant interactions [30,31,32,33,34,35]. Relatively little has yet been done for inter-species pathogen-host networks. Several common factors that have proved useful in other studies are 1) evaluating network hubs with many interactions and 2) using correlations between interacting pairs with similar gene expression patterns. For this small interactome, we looked for relatively abundant proteins associated with multiple interactions. We identified a single human protein interacting with three viral proteins, three being the largest number of viral interactions seen with a single host protein in this data set. The interactions are shown in Figure 5B. The host protein Keratin, type II cytoskeletal 4 (P19013) interacts with three viral proteins (P11258 - 14 kDa fusion protein, A27L; Q805H7 - Chemokine-binding protein C23/B29; P17362 - Protein C6L). The 14 kDa fusion protein A27L is the most abundant protein seen in this data set and participates in virus penetration at during cell fusion [36,37]. A27L facilitates initial attachment to cells by binding to glycosaminoglycans [38]. A27L is found in all orthopoxviruses and has no cellular or entomopoxvirus homologs. Additional viral proteins involved in attachment (D8L, H3L) [39,40] and fusion (F9L, I2L) [41,42] were not observed. The Chemokine-binding protein C23L belongs to a family of poxvirus PLoS ONE | www.plosone.org 6 September 2009 | Volume 4 | Issue 9 | e7162