Table S5 Top ten GO processes differentially regulated between virus and mock treatments in cells differentiated from apoE3/E3 NEP.

GO Process / Total genes in process / p value / Number of genes in active data / Genes in data
1 / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / 22 / 3.584E-18 / 13 / HLA-A2, 1B57_HUMAN, MHC class I, HLA-B7, HLAB, HLA-A3, HLA-A, HLA-B, HLA-A11, 1B35_HUMAN, 1B08_HUMAN, HLA-F, HLA-B27
2 / type I interferon-mediated signaling pathway / 85 / 1.313E-17 / 20 / HLA-A2, 1B57_HUMAN, RNaseL, MHC class I, HLA-B7, IFI17, HLAB, HLA-A3, IFI27, HLA-A, PSMB8(LMP7), HLA-B, HLA-A11, 1B35_HUMAN, STAT1, STAT2, 1B08_HUMAN, STAT1/STAT2, HLA-F, HLA-B27
3 / cellular response to type I interferon / 86 / 1.684E-17 / 20 / HLA-A2, 1B57_HUMAN, RNaseL, MHC class I, HLA-B7, IFI17, HLAB, HLA-A3, IFI27, HLA-A, PSMB8(LMP7), HLA-B, HLA-A11, 1B35_HUMAN, STAT1, STAT2, 1B08_HUMAN, STAT1/STAT2, HLA-F, HLA-B27
4 / response to type I interferon / 87 / 2.154E-17 / 20 / HLA-A2, 1B57_HUMAN, RNaseL, MHC class I, HLA-B7, IFI17, HLAB, HLA-A3, IFI27, HLA-A, PSMB8(LMP7), HLA-B, HLA-A11, 1B35_HUMAN, STAT1, STAT2, 1B08_HUMAN, STAT1/STAT2, HLA-F, HLA-B27
5 / antigen processing and presentation of exogenous peptide antigen / 136 / 1.181E-16 / 23 / MHC class II alpha chain, HLA-A2, Ubiquitin, Tapasin, 1B57_HUMAN, MHC class I, HLA-B7, HLAB, PSMB9, UBB, TAP1 (PSF1), HLA-A3, HLA-A, CD74, PSMB8(LMP7), HLA-B, ITGB5, HLA-A11, 1B35_HUMAN, IP-30, 1B08_HUMAN, HLA-F, HLA-B27
6 / antigen processing and presentation of endogenous antigen / 27 / 1.338E-16 / 13 / Tapasin, 1B57_HUMAN, MHC class I, HLA-B7, HLAB, TAP1 (PSF1), HLA-A, CD74, HLA-B, 1B35_HUMAN, 1B08_HUMAN, HLA-F, HLA-B27
7 / antigen processing and presentation of exogenous antigen / 141 / 2.701E-16 / 23 / MHC class II alpha chain, HLA-A2, Ubiquitin, Tapasin, 1B57_HUMAN, MHC class I, HLA-B7, HLAB, PSMB9, UBB, TAP1 (PSF1), HLA-A3, HLA-A, CD74, PSMB8(LMP7), HLA-B, ITGB5, HLA-A11, 1B35_HUMAN, IP-30, 1B08_HUMAN, HLA-F, HLA-B27
8 / antigen processing and presentation of exogenous peptide antigen via MHC class I / 115 / 5.075E-16 / 21 / HLA-A2, Ubiquitin, Tapasin, 1B57_HUMAN, MHC class I, HLA-B7, HLAB, PSMB9, UBB, TAP1 (PSF1), HLA-A3, HLA-A, PSMB8(LMP7), HLA-B, ITGB5, HLA-A11, 1B35_HUMAN, IP-30, 1B08_HUMAN, HLA-F, HLA-B27
9 / antigen processing and presentation of peptide antigen / 179 / 5.906E-16 / 25 / MHC class II alpha chain, HLA-A2, Ubiquitin, Tapasin, 1B57_HUMAN, MHC class I, HLA-B7, Puromycin-sensitive aminopeptidase, HLAB, PSMB9, UBB, NPEPPS, TAP1 (PSF1), HLA-A3, HLA-A, CD74, PSMB8(LMP7), HLA-B, ITGB5, HLA-A11, 1B35_HUMAN, IP-30, 1B08_HUMAN, HLA-F, HLA-B27
10 / antigen processing and presentation of peptide antigen via MHC class I / 153 / 1.717E-15 / 23 / HLA-A2, Ubiquitin, Tapasin, 1B57_HUMAN, MHC class I, HLA-B7, Puromycin-sensitive aminopeptidase, HLAB, PSMB9, UBB, NPEPPS, TAP1 (PSF1), HLA-A3, HLA-A, PSMB8(LMP7), HLA-B, ITGB5, HLA-A11, 1B35_HUMAN, IP-30, 1B08_HUMAN, HLA-F, HLA-B27

Genes were analyzed for GO processes using the MetaCoreÔ software on GeneGo from Thomson Reuters, including genes differentially expressed when comparing HIV-exposed vs. mock-exposed cultures. Only apoE3/E3 cultures were included in this analysis. p≤0.01