Lenge a single SR3029 Factor emerged as best able to discriminate symptomatic-infected subjects from asymptomatic-uninfected subjects at the time of maximal symptoms (Fig. 2). We derived this gene signature or “Influenza Factor” individually for both H1N1 and H3N2 andfound that the signature is highly conserved across the two different viruses. For H1N1, the derived factor correctly identifies our phenotypically confirmed individuals exposed to H1N1 as symptomatic-infected or asymptomatic-uninfected with only a single misclassification, whereas the H3N2 factor correctly identifies 100 of individuals exposed to H3N2 with a confirmed phenotype. The performance of two separate clinical challenge studies with closely related viruses permits the validation of the independently derived gene signatures by testing them on the subjects from the alternate study. When the factor loadings for H1N1 are applied to the subjects from the H3N2 study, the H1N1 factor is capable of accurately discriminating between symptomatic-infected or asymptomatic-uninfected H3N2 subjects 100 of the time (Fig. s3). Similarly, when applied to the H1N1 data set, the H3N2 factor correctly identifies 93 (14/15) of the subjects in the H1N1 study as symptomatic-infected or asymptomatic-uninfected. Thus, each of the independently derived factors for H1N1 or H3N2 performs well when applied to a completely separate data set 125-65-5 comprised of individuals with a similar yet distinct pathogen.Figure 2. Gene expression signatures expressed through factor scores. An influenza gene expression signature, or factor, evolves over time in symptomatic individuals (blue dots) and distinguishes between symptomatic and asymptomatic individuals (red dots) for both H1N1 (A) and H3N2 (B) viruses at later time points. Heat maps of the top 50 genes in the discriminative factor for H1N1 (c) and H3N2 (d) as they develop over time are shown. doi:10.1371/journal.pone.0052198.gHost Genomic Signatures Detect H1N1 InfectionFigure 3. Gene expression signature trajectory over time. The magnitude of the Influenza Factor varies from inoculation through resolution of disease, for both H1N1 (A) and H3N2 (B) patients. The average factor score at each timepoint for both symptomatic (blue) and asymptomatic (red) individuals are shown. The average time of symptom onset (gray dashed line) and maximal symptoms (black dashed line) are depicted. doi:10.1371/journal.pone.0052198.gDiscriminatory Factors for H1N1 and H3N2 are Similar and Include Genes Involved in the Antiviral ResponseThe gene signatures derived independently for the two different strains of influenza are highly similar, sharing 44 out of the top 50 genes (88 , Table s4). However, the importance of these few disparities is unclear, as the discordant genes are not sufficient to allow for differentiation between the two viruses in our analysis. When compared to our previous work with HRV and RSV, theInfluenza Factor shares only 65?9 of its genes with factors describing infection with these other respiratory viruses, suggesting both common `viral URI’ pathways as well as some degree of etiologic specificity. The majority of the top 50 predictive genes contained in each factor are known to characterize host response to viral infection, and include RSAD2, the OAS family, multiple interferon response elements, the myxovirus-resistance gene MX1, cytokine response pathways 12926553 and others [16,17,18]. Many (but notHost Genomic Signatures Detect H1N1 Infectionall) of the c.Lenge a single factor emerged as best able to discriminate symptomatic-infected subjects from asymptomatic-uninfected subjects at the time of maximal symptoms (Fig. 2). We derived this gene signature or “Influenza Factor” individually for both H1N1 and H3N2 andfound that the signature is highly conserved across the two different viruses. For H1N1, the derived factor correctly identifies our phenotypically confirmed individuals exposed to H1N1 as symptomatic-infected or asymptomatic-uninfected with only a single misclassification, whereas the H3N2 factor correctly identifies 100 of individuals exposed to H3N2 with a confirmed phenotype. The performance of two separate clinical challenge studies with closely related viruses permits the validation of the independently derived gene signatures by testing them on the subjects from the alternate study. When the factor loadings for H1N1 are applied to the subjects from the H3N2 study, the H1N1 factor is capable of accurately discriminating between symptomatic-infected or asymptomatic-uninfected H3N2 subjects 100 of the time (Fig. s3). Similarly, when applied to the H1N1 data set, the H3N2 factor correctly identifies 93 (14/15) of the subjects in the H1N1 study as symptomatic-infected or asymptomatic-uninfected. Thus, each of the independently derived factors for H1N1 or H3N2 performs well when applied to a completely separate data set comprised of individuals with a similar yet distinct pathogen.Figure 2. Gene expression signatures expressed through factor scores. An influenza gene expression signature, or factor, evolves over time in symptomatic individuals (blue dots) and distinguishes between symptomatic and asymptomatic individuals (red dots) for both H1N1 (A) and H3N2 (B) viruses at later time points. Heat maps of the top 50 genes in the discriminative factor for H1N1 (c) and H3N2 (d) as they develop over time are shown. doi:10.1371/journal.pone.0052198.gHost Genomic Signatures Detect H1N1 InfectionFigure 3. Gene expression signature trajectory over time. The magnitude of the Influenza Factor varies from inoculation through resolution of disease, for both H1N1 (A) and H3N2 (B) patients. The average factor score at each timepoint for both symptomatic (blue) and asymptomatic (red) individuals are shown. The average time of symptom onset (gray dashed line) and maximal symptoms (black dashed line) are depicted. doi:10.1371/journal.pone.0052198.gDiscriminatory Factors for H1N1 and H3N2 are Similar and Include Genes Involved in the Antiviral ResponseThe gene signatures derived independently for the two different strains of influenza are highly similar, sharing 44 out of the top 50 genes (88 , Table s4). However, the importance of these few disparities is unclear, as the discordant genes are not sufficient to allow for differentiation between the two viruses in our analysis. When compared to our previous work with HRV and RSV, theInfluenza Factor shares only 65?9 of its genes with factors describing infection with these other respiratory viruses, suggesting both common `viral URI’ pathways as well as some degree of etiologic specificity. The majority of the top 50 predictive genes contained in each factor are known to characterize host response to viral infection, and include RSAD2, the OAS family, multiple interferon response elements, the myxovirus-resistance gene MX1, cytokine response pathways 12926553 and others [16,17,18]. Many (but notHost Genomic Signatures Detect H1N1 Infectionall) of the c.
