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. 2015 Oct 20;11(10):e1004553. doi: 10.1371/journal.pcbi.1004553

Table 1. Ten molecular signatures from genomics data used for predicting novel RLR pathway components.

Group Molecular signature Data set description Type a References Number of genes b Likelihood ratio score b , c
Virus-based Positive selection in primates Rapidly evolving genes in the primates lineage, detected using maximum likelihood analysis of nucleotide alignments d [23] 926 1.7
PPI with viruses Virus-interacting human proteins extracted from PPI databases c [28] 2,587 4.2
Viral miRNA target Likelihood scores of targeting of human transcripts by viral miRNAs, based on predicted target sites c [30] 6,761 1.3
Differential expression upon infection Genes showing differential expression in lung epithelial cells infected with four respiratory viruses c see Methods 1,680 3.5
Antiviral host factor Meta analysis of genes with antiviral activity from seven RNAi screens studying a variety of viruses c see S3 Table 173 2.1
Pathway-based Co-expression with RLR pathway Weighted co-expression with known RLR genes across >450 human gene expression studies c [32] 4,149 2.4
RLR pathway protein domain Proteins containing one of the 25 domains that are significantly enriched in known RLR proteins c [66] 711 8.9
Innate antiviral TF binding motifs Genes with IRF, AP–1, NFκB, or STAT TF binding motifs in their promoters, based on conservation across 29 mammals c [33] 4,508 2.3
NFκB activation mediator Hits from a genome-wide siRNA screen of Epstein-Barr virus-induced NFκB activation d [34] 154 19.8
RLR pathway PPI Proteins that interact with known RLR proteins, calculated from PPI data c [35] 1,750 4.3
Integration RLR score Bayesian integration of the 10 molecular signatures to predict novel RLR pathway components

a Data used directly (d) or as basis for further calculation (c)

b Combination of all bins with positive likelihood ratio scores per feature, derived from Fig 1A

c RLR genes versus non-RLR genes: P(Di | RLR genes) / P(Di | non-RLR genes), see Methods.

Note that, to avoid circularity, the predictive ability of the co-expression, protein domain and RLR pathway PPI data sets was assessed using the set of TLR, CLR, NLR, cytDNA genes instead of the RLR genes (see Methods).

See also Fig 1A and S1 Table.