Table 2. Gene set enrichment analysis of DET signatures
Gene seta(threshold)Annotation setTermOverlapq‐valuebZ‐scoreCombined scorec
4163 DETs for timepoint: acute vs. convalescent (FCH > 2, < 0.05)GO Biological Process 2015Viral transcription71/84< 0.001−2.11152
Translational termination71/89< 0.001−2.11138
Translational elongation80/114< 0.001−2.12126
PANTHER 2016Apoptosis signaling pathway43/102< 0.001−1.6915.8
Toll receptor signaling pathway23/49< 0.001−1.398.6
T cell activation29/73< 0.001−1.397.1
Reactome 2016Eukaryotic translation elongation76/89< 0.001−2.10163
Peptide chain elongation72/84< 0.001−2.01151
Viral mRNA Translation70/84< 0.001−1.95136
681 DETs for viral titer (q < 0.1)GO Biological Process 2015Leukocyte activation38/373< 0.001−2.3729
Lymphocyte activation32/204< 0.001−2.3224
Regulation of leukocyte activation34/390< 0.001−2.5319
PANTHER 2016Endothelin signaling pathway27/5760.29−1.541.9
T cell activation26/8460.29−1.501.9
JAK/STAT signaling42/8080.28−1.441.8
Reactome 2016Adaptive immune system453/762< 0.001−2.2817
Infectious disease28/3480.005−2.3812
HIV infection21/2220.005−2.3712
  • DET, differentially expressed transcript; FCH, fold change; GO, gene ontology; HIV, human immunodeficiency virus.

  • a Gene sets were constructed by thresholding DETs at the specified FCH and q‐values and mapping to unique gene symbols.

  • b q‐values are P‐values adjusted using the Benjamini–Hochberg method, controlling the false discovery rate.

  • c Combined scores are the product of negative log P‐values and the Z‐score as described previously (Chen et al, 2013); the top three terms per annotation set, ordered by combined score, are displayed in this table.