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. 2015 Sep 15;43(3):605-14.
doi: 10.1016/j.immuni.2015.08.014. Epub 2015 Sep 8.

Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases

Dmitriy Gorenshteyn  1 , Elena Zaslavsky  2 , Miguel Fribourg  2 , Christopher Y Park  3 , Aaron K Wong  4 , Alicja Tadych  1 , Boris M Hartmann  2 , Randy A Albrecht  5 , Adolfo García-Sastre  6 , Steven H Kleinstein  7 , Olga G Troyanskaya  8 , Stuart C Sealfon  9
Affiliations

Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases

Dmitriy Gorenshteyn et al. Immunity. .

Abstract

Many functionally important interactions between genes and proteins involved in immunological diseases and processes are unknown. The exponential growth in public high-throughput data offers an opportunity to expand this knowledge. To unlock human-immunology-relevant insight contained in the global biomedical research effort, including all public high-throughput datasets, we performed immunological-pathway-focused Bayesian integration of a comprehensive, heterogeneous compendium comprising 38,088 genome-scale experiments. The distillation of this knowledge into immunological networks of functional relationships between molecular entities (ImmuNet), and tools to mine this resource, are accessible to the public at http://immunet.princeton.edu. The predictive capacity of ImmuNet, established by rigorous statistical validation, is easily accessed by experimentalists to generate data-driven hypotheses. We demonstrate the power of this approach through the identification of unique host-virus interaction responses, and we show how ImmuNet complements genetic studies by predicting disease-associated genes. ImmuNet should be widely beneficial for investigating the mechanisms of the human immune system and immunological diseases.

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Figures

Figure 1
Figure 1. ImmuNet Development and Selected Applications
Data from more than 38,000 experiments (including mRNA expression, protein interaction assays, and phenotypic assays) were collected from public repositories and systematically processed (see Supplemental Computational Methods). These data and curated immune pathway prior knowledge from KEGG were used as input to infer 15 immune-specific functional relationship networks and an overall Immune Global context averaged network. Each immune-specific functional network predicts functional association between molecular entities (genes or proteins) specific to a particular immune biological process (e.g., antigen processing and presentation). ImmuNet leverages this massive data compendium to predict novel immune process or immune disease associations. See Supplemental Computational Methods for full information on the data compendium and integration.
Figure 2
Figure 2. ImmuNet Accurately Recapitulates Known Functional Relationships in Immune Pathways
(A) ImmuNet networks were evaluated via 3-fold cross-validation. For each pathway, one-third of the pathway data was iteratively omitted when constructing the network and the accuracy of this network in predicting the held-out information was tested. The panel shows the successful recovery of held-out immune data when we used the standard area-under receiver operator curve (AUC) metric that reflects both specificity and sensitivity (Hastie et al., 2011). Bar plots represent the mean ± SEM of the three cross-validations. (B) Using 3-fold cross-validation, the performance of the ImmuNet global network was compared to two standard non-immune-specific networks, BioGRID PPI network and a functional integration Human Global network. Boxplots represent the AUC performance distribution of each network at recovering known immune relationships (from the 15 KEGG contexts) that were held out during the training of each network. ImmuNet significantly outperformed the other two networks. p values are based on Wilcoxon signed-rank test. See also Figure S1 and Table S1.
Figure 3
Figure 3. Illustration of the Use of Immune-Specific Functional Networks
(A) High-confidence subnetwork obtained by querying the ImmuNet hematopoietic cell lineage network with IFNAR1 (Interferon receptor 1) and FAS (Cell surface death receptor). The subnetwork obtained predicted that the processes reflected by the query genes are functionally related to PTGER2 and MNDA. The visualization parameters used to generate the graph shown are minimum relationship confidence = 0.61 and maximum number of genes = 21. (B) The relationship of MNDA to cell death in the context of antiviral responses was evaluated by comparing its induction by infection of DCs by IAV that induce cell death (seasonal viruses NC/99; TX/91) or do not induce cell death (pandemic viruses Brevig, Cal/09) in these cells. Data shown is 8 hr after infection at MOI = 1, normalized to the levels obtained with vehicle-treated cells. Notably, MNDA is differentially induced by the two virus groups. Bar plots represent the mean ± SEM gene expression fold-change of three replicate infections. See also Table S2.
Figure 4
Figure 4. Functional Networks Predict Specificity of Influenza Viral Infection
(A) Pathogenic viruses, such as the NC/99 IAV strain, have developed immune antagonist mechanisms to suppress components of the antiviral response gene program. Genes induced in human DCs infected with NC/99 (Zaslavsky et al., 2013) were used as input for an ImmuNet-based method to predict differential absence genes. With these 183 genes as positive examples, an SVM classifier was trained to identify genes in the Immune Global network that were closely related to the seed set but were not induced by NC/99. The absence of these “expected” genes identified them as candidates for NC/99 immune antagonist mechanisms. (B) DCs were infected at MOI = 1 with NC/99 or NDV. Infectivity was assayed by immunostaining of viral proteins (NP for NC/99 and HN for NDV). Antiviral gene MX1 was induced by each virus, assayed by RT-PCR, indicating virus detection and initiation of cellular responses. (C) Expression levels of the 16 SVM-classifier top-ranked “expected” absence genes 8 hr after NC/99 or NDV infection were assayed. Seven of the predicted genes were significantly higher after NDV infection at 8 hr (p < 0.05). Data represent mean ± SEM from three independent experiments, each performed in triplicate.
Figure 5
Figure 5. Immune-Specific Functional Networks Accurately Predict Gene-Disease Associations
To predict disease-associated genes, SVM classifiers were trained using ImmuNet with OMIM genes annotated to CVID, IBD, and RA. (A) Results of 3-fold cross-validation, in which each classifier was trained without one-third of the known positives, and the accuracy of predicting this held-out information was evaluated by receiver-operator AUC. (B) Prediction of GWAS-associated genes by ImmuNet classifiers. The relationships of the SVM classifier score and reported GWAS-associated genes were determined. The graph shows differences in the probability density of genes reported as GWAS associated in comparison with other genes in the network. Genes with high SVM scores were highly significantly enriched in reported GWAS-associated genes for all three diseases. (C) Prediction of reported IBD eQTL genes by ImmuNet IBD classifier. The relationship of the SVM classifier scores and reported eQTL genes was determined. The graph shows a significant difference in the probability density of genes identified by eQTL analysis in comparison with other genes in the network. See also Figure S2 and Table S3.
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