Protein lists identified in untreated and/or IFN-γ–treated groups were converted to gene lists that were submitted to the Metascape database (67, 68), a gene annotation and analysis resource (http://metascape.org/), for pathway and process enrichment analysis. For each given gene list, Metascape carries pathway and process enrichment analysis using the following ontology sources: GO biological processes, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and Reactome gene sets. All genes in the genome were used as the enrichment background. Terms with P < 0.01, a minimum count of 3, and an enrichment factor of >1.5 are collected and grouped into clusters based on their membership similarities. More specifically, P values are calculated on the basis of accumulative hypergeometric distribution, and q values are calculated using the Benjamini-Hochberg procedure to account for multiple testing. κ scores were used as the similarity metric when performing hierarchical clustering on the enriched terms, and then, subtrees with similarity > 0.3 are considered a cluster. The most statistically significant term within a cluster is chosen as the one representing the cluster.

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